Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/v/vg/vg_1.30.0+ds-1+b2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/vg-1.30.0+ds-1+b2ltqxicg6/vg_1.30.0+ds-1+b2_amd64.buildinfo Get source package info: vg=1.30.0+ds-1 Source URL: http://snapshot.notset.fr/mr/package/vg/1.30.0+ds-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 bc=1.07.1-3+b1 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bison=2:3.8.2+dfsg-1 bsdextrautils=2.38-4 bsdmainutils=12.1.7+nmu3 bsdutils=1:2.38-4 build-essential=12.9 bwa=0.7.17-7 bzip2=1.0.8-5 ca-certificates=20211016 cmake=3.23.1-2 cmake-data=3.23.1-2 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docbook=4.5-9 docbook-to-man=1:2.0.0-45 docbook-xml=4.5-11 docbook-xsl=1.79.2+dfsg-1 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 elfutils=0.186-1 emacsen-common=3.0.4 fastahack=1.0.0+dfsg-9 file=1:5.41-4 findutils=4.9.0-3 flex=2.6.4-8 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.3.0-1 gawk=1:5.1.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12-20220428-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gtk-doc-tools=1.33.2-1 gzip=1.12-1 help2man=1.49.2 hostname=3.23 icu-devtools=71.1-2 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 jq=1.6-2.1 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.6.0-1 libasan6=11.3.0-1 libasm1=0.186-1 libatomic1=12-20220428-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbackward-cpp-dev=1.6-1 libbinutils=2.38-3 libblas3=3.10.1-1 libblkid-dev=2.38-4 libblkid1=2.38-4 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-14+b1 libboost-program-options1.74.0=1.74.0-14+b1 libboost1.74-dev=1.74.0-14+b1 libbrotli-dev=1.0.9-2+b3 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libbz2-dev=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo-gobject2=1.16.0-5 libcairo-script-interpreter2=1.16.0-5 libcairo2=1.16.0-5 libcairo2-dev=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220428-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl3-gnutls=7.83.0-1 libcurl4=7.83.0-1 libcurl4-gnutls-dev=7.83.0-1 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate-dev=1.10-2 libdeflate0=1.10-2 libdisorder-dev=0.0.2+git20130809.8062ee1-4 libdisorder0=0.0.2+git20130809.8062ee1-4 libdivsufsort-dev=2.0.1-5 libdivsufsort3=2.0.1-5 libdpkg-perl=1.21.7 libdw-dev=0.186-1 libdw1=0.186-1 libelf-dev=0.186-1 libelf1=0.186-1 libexpat1=2.4.8-1 libexpat1-dev=2.4.8-1 libfastahack-dev=1.0.0+dfsg-9 libfastahack0=1.0.0+dfsg-9 libffi-dev=3.4.2-4 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfml-dev=0.1+git20190320.b499514-1+b1 libfml0=0.1+git20190320.b499514-1+b1 libfontconfig-dev=2.13.1-4.4 libfontconfig1=2.13.1-4.4 libfontconfig1-dev=2.13.1-4.4 libfreetype-dev=2.11.1+dfsg-2 libfreetype6=2.11.1+dfsg-2 libfreetype6-dev=2.11.1+dfsg-2 libfribidi0=1.0.8-2.1 libgcc-11-dev=11.3.0-1 libgcc-s1=12-20220428-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran5=12-20220428-1 libglib2.0-0=2.72.1-1 libglib2.0-bin=2.72.1-1 libglib2.0-data=2.72.1-1 libglib2.0-dev=2.72.1-1 libglib2.0-dev-bin=2.72.1-1 libgmp-dev=2:6.2.1+dfsg-3 libgmp10=2:6.2.1+dfsg-3 libgmpxx4ldbl=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12-20220428-1 libgpg-error0=1.45-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1+b1 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.2.1-1 libice-dev=2:1.0.10-1 libice6=2:1.0.10-1 libicu-dev=71.1-2 libicu71=71.1-2 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12-20220428-1 libjansson-dev=2.14-2 libjansson4=2.14-2 libjbig0=2.1-3.1+b2 libjemalloc-dev=5.2.1-4 libjemalloc2=5.2.1-4 libjpeg62-turbo=1:2.1.2-1 libjq1=1.6-2.1 libjsoncpp25=1.9.5-4 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack3=3.10.1-1 libldap-2.5-0=2.5.11+dfsg-1 liblocale-gettext-perl=1.07-4+b2 liblsan0=12-20220428-1 libltdl7=2.4.7-3 liblz4-1=1.9.3-2 liblz4-dev=1.9.3-2 liblzma-dev=5.2.5-2.1 liblzma5=5.2.5-2.1 liblzo2-2=2.10-2 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmd0=1.0.4-1 libmhash2=0.9.9.9-9 libmount-dev=2.38-4 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses-dev=6.3+20220423-1 libncurses5-dev=6.3+20220423-1 libncurses6=6.3+20220423-1 libncursesw6=6.3+20220423-1 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libonig5=6.9.7.1-2 libosp5=1.5.2-13+b2 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpango-1.0-0=1.50.6+ds-2 libpangocairo-1.0-0=1.50.6+ds-2 libpangoft2-1.0-0=1.50.6+ds-2 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre16-3=2:8.39-14 libpcre2-16-0=10.40-1 libpcre2-32-0=10.40-1 libpcre2-8-0=10.40-1 libpcre2-dev=10.40-1 libpcre2-posix3=10.40-1 libpcre3=2:8.39-14 libpcre3-dev=2:8.39-14 libpcre32-3=2:8.39-14 libpcrecpp0v5=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libpixman-1-dev=0.40.0-1 libpng-dev=1.6.37-5 libpng16-16=1.6.37-5 libprocps8=2:3.3.17-7+b1 libprotobuf-dev=3.12.4-1+b3 libprotobuf-lite23=3.12.4-1+b3 libprotobuf23=3.12.4-1+b3 libprotoc-dev=3.12.4-1+b3 libprotoc23=3.12.4-1+b3 libpsl5=0.21.0-1.2 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.10.4-1+b1 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libquadmath0=12-20220428-1 libraptor2-0=2.0.14-1.2 libraptor2-dev=2.0.14-1.2 librasqal3=0.9.33-0.2 librasqal3-dev=0.9.33-0.2 librdf0=1.0.17-1.1+b1 librdf0-dev=1.0.17-1.1+b1 libreadline8=8.1.2-1.2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4 libsasl2-modules-db=2.1.28+dfsg-4 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libselinux1-dev=3.3-1+b2 libsepol-dev=3.3-1 libsepol2=3.3-1 libsigsegv2=2.14-1 libsimde-dev=0.7.2-6 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.38-4 libsmithwaterman-dev=0.0+git20160702.2610e25-12 libsmithwaterman0=0.0+git20160702.2610e25-12 libsparsehash-dev=2.0.3-2 libsqlite3-0=3.38.3-1 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libssw-dev=1.1-13 libssw0=1.1-13 libstdc++-11-dev=11.3.0-1 libstdc++6=12-20220428-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtabixpp-dev=1.1.0-6 libtabixpp0=1.1.0-6 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtiff5=4.3.0-7 libtinfo6=6.3+20220423-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.7-3 libtsan0=11.3.0-1 libtsl-hopscotch-map-dev=2.3.0-2 libubsan1=12-20220428-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-4 libuv1=1.44.1-2 libvcflib-dev=1.0.3+dfsg-1 libvcflib-tools=1.0.3+dfsg-1 libvcflib1=1.0.3+dfsg-1 libwebp7=1.2.2-2+b1 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libx11-dev=2:1.7.5-1 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-render0-dev=1.14-3 libxcb-shm0=1.14-3 libxcb-shm0-dev=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.4-1 libxext6=2:1.3.4-1 libxft2=2.3.4-1 libxml2=2.9.13+dfsg-1+b1 libxml2-dev=2.9.13+dfsg-1+b1 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libxslt1-dev=1.1.34-4 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libxt6=1:1.2.1-1 libyajl-dev=2.1.0-3 libyajl2=2.1.0-3 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 littler=0.3.15-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.1.0 ncal=12.1.7+nmu3 ncurses-base=6.3+20220423-1 ncurses-bin=6.3+20220423-1 opensp=1.5.2-13+b2 openssl=1.1.1n-1 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-7+b1 protobuf-compiler=3.12.4-1+b3 pv=1.6.20-1 python3=3.10.4-1+b1 python3-distutils=3.9.12-1 python3-lib2to3=3.9.12-1 python3-lxml=4.8.0-1 python3-minimal=3.10.4-1+b1 python3-pkg-resources=59.6.0-1.2 python3-pygments=2.11.2+dfsg-2 python3.10=3.10.4-3 python3.10-minimal=3.10.4-3 r-base-core=4.2.0-1+b1 r-cran-cli=3.2.0-1 r-cran-colorspace=2.0-3+dfsg-1 r-cran-crayon=1.5.1-1 r-cran-digest=0.6.29-1 r-cran-ellipsis=0.3.2-2 r-cran-fansi=1.0.3-1 r-cran-farver=2.1.0-1 r-cran-ggplot2=3.3.5+dfsg-5 r-cran-glue=1.6.2-1 r-cran-gridbase=0.4-7-5 r-cran-gtable=0.3.0+dfsg-2 r-cran-isoband=0.2.5-1 r-cran-labeling=0.4.2-1 r-cran-lattice=0.20-45-3 r-cran-lifecycle=1.0.1-1 r-cran-littler=0.3.15-1 r-cran-magrittr=2.0.2-1 r-cran-mass=7.3-57-1 r-cran-matrix=1.4-1-1 r-cran-mgcv=1.8-40-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.157-1 r-cran-pillar=1.7.0+dfsg-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.2-2 r-cran-plyr=1.8.6-2 r-cran-r6=2.5.1-1 r-cran-rcolorbrewer=1.1-3-1 r-cran-rcpp=1.0.8.3-1 r-cran-rlang=1.0.2-1 r-cran-scales=1.1.1-1 r-cran-tibble=3.1.6+dfsg-1 r-cran-utf8=1.2.2-1 r-cran-vctrs=0.3.8-2 r-cran-viridislite=0.4.0-2 r-cran-withr=2.5.0-1 rapidjson-dev=1.1.0+dfsg2-7 raptor2-utils=2.0.14-1.2 rasqal-utils=0.9.33-0.2 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 rs=20200313-1 samtools=1.13-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sgml-data=2.0.11+nmu1 sysvinit-utils=3.03-1 tabix=1.13+ds-2 tar=1.34+dfsg-1 tzdata=2022a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.38-4 util-linux-extra=2.38-4 uuid-dev=2.38-4 x11-common=1:7.7+23 x11proto-dev=2022.1-1 xdg-utils=1.1.3-4.1 xml-core=0.18+nmu1 xorg-sgml-doctools=1:1.11-1.1 xsltproc=1.1.34-4 xtrans-dev=1.4.0-1 xxd=2:8.2.4793-1 xz-utils=5.2.5-2.1 zip=3.0-12 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220629T212513Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220501T215056Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-962s5Z && dpkg-source --no-check -x /*.dsc /build/vg-962s5Z/vg-1.30.0+ds && cd /build/vg-962s5Z/vg-1.30.0+ds && { printf '%s' 'vg (1.30.0+ds-1+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 01 May 2022 23:59:58 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/vg-962s5Z" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-962s5Z/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651449598" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/vg-962s5Z /tmp/vg-1.30.0+ds-1+b2ltqxicg6 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.9litwyy3Qn as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.9litwyy3Qn Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (992 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4627 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220629T212513Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220501T215056Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.9litwyy3Qn Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220629T212513Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220629T212513Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220629T212513Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220629T212513Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220629T212513Z unstable/main amd64 Packages [12.5 MB] Fetched 35.2 MB in 29s (1221 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.9litwyy3Qn I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-962s5Z && dpkg-source --no-check -x /*.dsc /build/vg-962s5Z/vg-1.30.0+ds && cd /build/vg-962s5Z/vg-1.30.0+ds && { printf '%s' 'vg (1.30.0+ds-1+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 01 May 2022 23:59:58 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/vg-962s5Z"' exec /tmp/mmdebstrap.9litwyy3Qn Reading package lists... NOTICE: 'vg' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vg.git Please use: git clone https://salsa.debian.org/med-team/vg.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 95.1 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (dsc) [2979 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (tar) [95.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (diff) [114 kB] Fetched 95.1 MB in 1min 17s (1242 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'vg_1.30.0+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting vg in /build/vg-962s5Z/vg-1.30.0+ds dpkg-source: info: unpacking vg_1.30.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.30.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-10 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_ssw dpkg-source: info: applying use_packaged_rapidjson dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying spelling dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying use_packaged_smithwaterman dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 dpkg-source: info: applying fix-handlegraph I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-962s5Z/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651449598" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.9litwyy3Qn dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.30.0+ds-1+b2 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' find /build/vg-962s5Z/vg-1.30.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j10 clean make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -rf ../bin ../lib cd cutest && make clean cd quicktree_1.1 && make clean make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_auto_clean: error: make -j10 clean returned exit code 2 make[1]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_autoreconf --sourcedirectory=/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level configure.ac:15: installing './compile' configure.ac:13: installing './config.guess' configure.ac:13: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/debian/help mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/debian/vg/usr mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/debian/vg/usr/lib/vg for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} all test/build_graph bin/shuf ; \ done make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" ./install.sh /build/vg-962s5Z/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-962s5Z/vg-1.30.0+ds/obj && cp src/*.h /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-962s5Z/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-962s5Z/vg-1.30.0+ds/include/ rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/vg-962s5Z/vg-1.30.0+ds' cp deps/BBHash/BooPHF.h /build/vg-962s5Z/vg-1.30.0+ds/include rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cp -r deps/sparsepp/sparsepp include/ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* touch lib/cleaned_old_boost cd quicktree_1.1 && make all CC="gcc -std=c99" rm -Rf include/google/protobuf deps/protobuf rm -Rf include/dynamic.hpp include/dynamic touch lib/cleaned_old_protobuf_v003 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/vg-962s5Z/vg-1.30.0+ds/include/ cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi CMake Warning (dev) at /usr/share/cmake-3.23/Modules/GNUInstallDirs.cmake:241 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c cp ./deps/gfakluge/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/ if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi find bin obj lib -type f -delete if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' cd ./deps/lru_cache && cp *.h* /build/vg-962s5Z/vg-1.30.0+ds/include/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi cp deps/sha1/*.h* /build/vg-962s5Z/vg-1.30.0+ds/include/ if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Setting build type to 'Debug' as none was specified. cp deps/progress_bar/progress_bar.hpp /build/vg-962s5Z/vg-1.30.0+ds/include g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- The C compiler identification is GNU 11.3.0 -- The C compiler identification is GNU 11.3.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -- The CXX compiler identification is GNU 11.3.0 ar rc cuTest.a *.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -- The C compiler identification is GNU 11.3.0 ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- The CXX compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 ranlib cuTest.a rm -f *.o -- Detecting C compiler ABI info mv cuTest.a ../../lib/ -- Detecting C compiler ABI info cp CuTest.h ../../lib/ -- Detecting CXX compiler ABI info make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Detecting C compiler ABI info - done gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Detecting CXX compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done libhandlegraph is root project or external_project -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG -- Configuring done gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Generating done ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Building in Debug mode -- Configuring done -- Generating done g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC -B/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake --color= g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 7%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/debug.cpp -- Performing Test HAVE_CXA_DEMANGLE /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake --color= gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 14%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h -- Performing Test HAVE_CXA_DEMANGLE - Success g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp -r deps/dozeu/simde include cp inc/sonLibString.h ../lib/sonLibString.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h -- Looking for C++ include cstdio cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ -- Looking for C++ include cstdio - found cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 21%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp -- Generating done [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 28%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/debug.dir/debug.cpp.o -o debug [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 28%] Built target debug [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ ar rc /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ranlib /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ [ 35%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -MF CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o.d -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/h0_lz77.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Linking CXX executable rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 50%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -MF CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o.d -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/rle_bwt.cpp [ 57%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 57%] Built target rle_lz77_v1 [ 57%] Built target rle_lz77_v2 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 96%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/ranlib libhandlegraph.a In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C diff: include/vg_environment_version.hpp: No such file or directory [ 64%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-962s5Z/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 64%] Built target rle_bwt g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp [ 71%] Built target h0_lz77 make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 78%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/cw-bwt.cpp ranlib sonLib.a [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 ln -s `which shuf` bin/shuf gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/lib/libvw.* /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm rm -f /build/vg-962s5Z/vg-1.30.0+ds/include/vg.pb.h /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/dozeu && cp deps/dozeu/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/dozeu/ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [ 85%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /usr/bin/c++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -MD -MT CMakeFiles/benchmark.dir/benchmark.cpp.o -MF CMakeFiles/benchmark.dir/benchmark.cpp.o.d -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/benchmark.cpp libtoolize: copying file 'acinclude.d/ltoptions.m4' mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' -- The CXX compiler identification is GNU 11.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:343 ] Protobuf_USE_STATIC_LIBS = OFF -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:479 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:487 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:505 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:519 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.13+ds -- Checking for module 'jansson' -- Found jansson, version 2.14 -- Configuring done [100%] Linking CXX static library libsdsl.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 7%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append [ 11%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 16%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 19%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 21%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 23%] Performing configure step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments CMake Warning (dev) at /usr/share/cmake-3.23/Modules/GNUInstallDirs.cmake:241 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info /usr/bin/ranlib libsdsl.a -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info configure.ac:15: installing './compile' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 26%] Performing build step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/handle.cpp configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... [100%] Built target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/*' yes rm -f '/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks checking whether make supports nested variables... make -f CMakeFiles/Makefile2 all yes make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build checking whether the C++ compiler works... make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp yes checking for C++ compiler default output file name... a.out -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp checking for suffix of executables... -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-962s5Z/vg-1.30.0+ds/include'. The library files are located in '/build/vg-962s5Z/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp checking whether we are cross compiling... [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= no checking for suffix of object files... make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp yes checking for g++ option to enable C++11 features... make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' none needed checking whether make supports the include directive... [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake yes (GNU style) checking dependency style of g++... /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 [ 92%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o gcc3 checking how to run the C++ preprocessor... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' g++ -E /usr/bin/ranlib libhandlegraph.a checking build system type... [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc [ 92%] Built target benchmark make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... [ 38%] Performing install step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp yes checking for gcc option to enable C11 features... make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= none needed checking whether gcc understands -c and -o together... make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' yes checking dependency style of gcc... [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install gcc3 checking for a sed that does not truncate output... [ 45%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /bin/sed checking for grep that handles long lines and -e... /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done /bin/grep -F checking for ld used by gcc... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... [ 45%] Built target handlegraph . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-962s5Z/vg-1.30.0+ds/lib BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... [100%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 1572864 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dbg.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' [100%] Built target cw-bwt make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles 0 @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/vg-962s5Z/vg-1.30.0+ds/deps/DYNAMIC/include/* include/dynamic /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ yes /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ checking for unistd.h... /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c lcp.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for dlfcn.h... yes checking for objdir... .libs In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_graph.cpp no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking how to run the C++ preprocessor... g++ -E make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 50%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /bin/grep -E In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:18: required from here /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands [ 59%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... [ 66%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 71%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking for stdint.h... [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... 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(cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /bin/grep -E checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' yes [ 88%] Built target vgio_static [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp checking that generated files are newer than configure... done configure: creating ./config.status [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c fast_locate.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating libvw.pc . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-962s5Z/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-962s5Z/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib . ./source_me.sh && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-962s5Z/vg-1.30.0+ds/include:/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" make && cp lib/libbdsg.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-962s5Z/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all config.status: creating vowpalwabbit/config.h make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' config.status: executing depfiles commands g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o config.status: executing libtool commands ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I .//../sonLib/lib/ -c impl/*.c rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -L/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib -Wl,-rpath,/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson -lhandlegraph -ldl rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio_static make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake config.status: creating vowpalwabbit/config.h -- Install configuration: "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc -- Set runtime path of "/build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c test.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c variants.cpp depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c benchmark.cpp depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwtgraph.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c minimizer.cpp depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_cover.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa2gbwt.cpp depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src 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-I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 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parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem 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-I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type 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../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx2 -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx2 -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/vw_exception.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:27: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o bin/vg-avx2 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" ./install.sh /build/vg-962s5Z/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-962s5Z/vg-1.30.0+ds/obj && cp src/*.h /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-962s5Z/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-962s5Z/vg-1.30.0+ds/include/ rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi Library will be installed in '/build/vg-962s5Z/vg-1.30.0+ds' rm -Rf include/boost if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" if [ ! -d lib ]; then mkdir -p lib; fi make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc find bin obj lib -type f -delete make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi touch lib/cleaned_old_boost if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi if [ ! -d obj ]; then mkdir -p obj; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o if [ ! -d lib ]; then mkdir -p lib; fi CMake Warning (dev) at /usr/share/cmake-3.23/Modules/GNUInstallDirs.cmake:241 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o rm -Rf include/google/protobuf deps/protobuf libhandlegraph is root project or external_project -- Configuring done g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. touch lib/cleaned_old_protobuf_v003 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-962s5Z/vg-1.30.0+ds/obj gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o ar rc cuTest.a *.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o ranlib cuTest.a -- The CXX compiler identification is GNU 11.3.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h -- The C compiler identification is GNU 11.3.0 cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h -- Detecting CXX compiler ABI info cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/lib/libvw.* /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac rm -f /build/vg-962s5Z/vg-1.30.0+ds/include/vg.pb.h /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- The CXX compiler identification is GNU 11.3.0 [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp -- Detecting CXX compiler ABI info [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE -- Detecting CXX compiler ABI info - done [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:343 ] Protobuf_USE_STATIC_LIBS = OFF -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:479 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:487 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:505 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:519 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp -- Found htslib, version 1.13+ds -- Checking for module 'jansson' -- Found jansson, version 2.14 -- Generating done # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all -- Configuring done make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= -- Generating done make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append ar rc /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 11%] Performing configure step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments ranlib /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a -- Configuring done [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure configure.ac:15: installing './compile' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' configure.ac:3: installing './missing' [ 14%] Performing build step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz make -f CMakeFiles/Makefile2 all cluster/Makefile.am: installing './depcomp' make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp [ 16%] Performing install step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/vg.proto cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level [ 26%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp checking whether the C++ compiler works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for C++ compiler default output file name... a.out checking for suffix of executables... [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp none needed [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o checking whether make supports the include directive... /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp yes (GNU style) checking dependency style of g++... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking how to run the C++ preprocessor... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ checking build system type... /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether gcc understands -c and -o together... [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... [ 30%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... [ 33%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 [ 35%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp checking for mt... no checking if : is a manifest tool... no checking for stdio.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for stdint.h... yes checking for strings.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/stat.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/types.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 38%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc static flag -static works... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C no checking dynamic linker characteristics... [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a checking for ld used by g++... make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend rm *.o /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... mv sonLib.a ../lib/ make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= yes gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 40%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /bin/grep -E checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... [ 45%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes [ 47%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp checking that generated files are newer than configure... done configure: creating ./config.status [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 50%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' config.status: creating cluster/Makefile [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o config.status: creating library/Makefile /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes [ 57%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o checking for a race-free mkdir -p... /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 59%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' yes checking dependency style of gcc... [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o [ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph 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[100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... /usr/bin/ranlib libhandlegraph.a 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [100%] Built target handlegraph_static cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp yes checking for stdlib.h... yes checking for string.h... [ 64%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... [ 66%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E [ 69%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 71%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /bin/grep -E checking whether the Boost::Program_Options library is available... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking for main in -lboost_program_options... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... [ 78%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... [ 80%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp checking that generated files are newer than configure... done configure: creating ./config.status [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 90%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 90%] Built target vgio [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-962s5Z/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-962s5Z/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c [ 95%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating Makefile ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I .//../sonLib/lib/ -c impl/*.c config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a Making all in vowpalwabbit ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 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--mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 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CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o /usr/bin/ranlib libvgio.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat 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-I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o Consolidate compiler generated dependencies of target vgio_static make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o make -f CMakeFiles/Makefile2 preinstall libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 -- Set runtime path of "/build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include/vg -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o [100%] Linking CXX static library libsdsl.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [100%] Built target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ Consolidate compiler generated dependencies of target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-962s5Z/vg-1.30.0+ds/include'. The library files are located in '/build/vg-962s5Z/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gcsa.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c lcp.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_graph.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:18: required from here /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c bwtmerge.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dynamic_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c fast_locate.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c test.cpp In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_ri.cpp In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-962s5Z/vg-1.30.0+ds/include:/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" make && cp lib/libbdsg.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-962s5Z/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa.cpp In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c minimizer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_cover.cpp depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa2gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman 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/usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem 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-I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:27: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o bin/vg-avx obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" ./install.sh /build/vg-962s5Z/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-962s5Z/vg-1.30.0+ds/obj && cp src/*.h /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-962s5Z/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-962s5Z/vg-1.30.0+ds/include/ rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/vg-962s5Z/vg-1.30.0+ds' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c if [ ! -d obj ]; then mkdir -p obj; fi WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d lib ]; then mkdir -p lib; fi make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all find bin obj lib -type f -delete rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc touch lib/cleaned_old_boost make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* rm -Rf include/google/protobuf deps/protobuf gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d obj ]; then mkdir -p obj; fi cd quicktree_1.1 && make all CC="gcc -std=c99" touch lib/cleaned_old_protobuf_v003 if [ ! -d lib ]; then mkdir -p lib; fi make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. libhandlegraph is root project or external_project -- Configuring done if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-962s5Z/vg-1.30.0+ds/obj if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp -- The CXX compiler identification is GNU 11.3.0 gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- The C compiler identification is GNU 11.3.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -- Detecting CXX compiler ABI info gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/lib/libvw.* /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./autogen.sh || true mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp ./autogen.sh: 22: [[: not found mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c rm -f /build/vg-962s5Z/vg-1.30.0+ds/include/vg.pb.h /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' -- The CXX compiler identification is GNU 11.3.0 -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' -- Detecting CXX compiler ABI info libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' -- Performing Test HAVE_CXA_DEMANGLE libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:343 ] Protobuf_USE_STATIC_LIBS = OFF cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp -- Configuring done [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:479 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:487 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:505 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:519 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.13+ds -- Checking for module 'jansson' -- Found jansson, version 2.14 [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp -- Configuring done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rc /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -- Generating done [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake configure.ac:15: installing './compile' configure.ac:3: installing './missing' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 ranlib /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= cluster/Makefile.am: installing './depcomp' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 11%] Performing configure step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp -- Configuring done [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 14%] Performing build step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= [ 66%] Built target handlegraph_shared make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles impl/sonLibCompression.c: In function ‘stCompression_compress’: /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for C++ compiler default output file name... a.out checking for suffix of executables... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp checking whether we are cross compiling... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C no checking for suffix of object files... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking how to run the C++ preprocessor... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking build system type... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking whether the compiler supports GNU C... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 26%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking for a sed that does not truncate output... [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o /bin/sed cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... [ 28%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 30%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' yes checking for string.h... [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= yes checking for inttypes.h... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o yes checking for stdint.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for strings.h... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' yes checking for sys/stat.h... [ 96%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= yes checking for sys/types.h... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for unistd.h... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' yes checking for dlfcn.h... [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o yes checking for objdir... .libs /usr/bin/ranlib libhandlegraph.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp checking if gcc supports -fno-rtti -fno-exceptions... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' yes checking if gcc static flag -static works... [ 33%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C no checking dynamic linker characteristics... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... [ 35%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /bin/grep -E checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... [ 38%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 40%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for exit in -lboost_program_options... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... [ 42%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp yes checking for joinable pthread attribute... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o yes ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 checking that generated files are newer than configure... done configure: creating ./config.status [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 45%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 47%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 50%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 52%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 54%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm config.status: creating Makefile config.status: creating vowpalwabbit/Makefile mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-962s5Z/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-962s5Z/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib config.status: creating vowpalwabbit/config.h make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c config.status: executing depfiles commands [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp config.status: executing libtool commands make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I .//../sonLib/lib/ -c impl/*.c In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 59%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 61%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 61%] Built target vgio [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking whether we are cross compiling... ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a no checking for suffix of object files... o checking whether the compiler supports GNU C++... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp yes checking whether g++ accepts -g... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp gcc3 checking how to run the C++ preprocessor... g++ -E [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 66%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp checking whether the compiler supports GNU C... [ 69%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... [ 71%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' [ 78%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 80%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp /bin/dd bs=4096 count=1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... [ 90%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking if gcc supports -c -o file.o... [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp yes checking if gcc supports -c -o file.o... 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[100%] Linking CXX static library libsdsl.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... 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[100%] Built target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= yes checking for joinable pthread attribute... Consolidate compiler generated dependencies of target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 PTHREAD_CREATE_JOINABLE make -f CMakeFiles/Makefile2 preinstall checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp yes -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-962s5Z/vg-1.30.0+ds/include'. The library files are located in '/build/vg-962s5Z/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-962s5Z/vg-1.30.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-962s5Z/vg-1.30.0+ds/lib . ./source_me.sh && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-962s5Z/vg-1.30.0+ds/include:/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" make && cp lib/libbdsg.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-962s5Z/vg-1.30.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dbg.cpp make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' checking that generated files are newer than configure... done configure: creating ./config.status make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c bwtmerge.cpp [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio_static make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so config.status: creating Makefile In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ -- Set runtime path of "/build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include/vg /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake config.status: creating vowpalwabbit/Makefile make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwt.cpp config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gcsa.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c lcp.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:18: required from here /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c test.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c variants.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c merge_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c benchmark.cpp depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c remove_seq.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time 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-D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa.cpp In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c minimizer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_cover.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. 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comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include 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/usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:27: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o bin/vg-sse4.1 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" ./install.sh /build/vg-962s5Z/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-962s5Z/vg-1.30.0+ds/obj && cp src/*.h /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-962s5Z/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-962s5Z/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi Library will be installed in '/build/vg-962s5Z/vg-1.30.0+ds' rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' find bin obj lib -type f -delete make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi touch lib/cleaned_old_boost rm -Rf include/google/protobuf deps/protobuf make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi cd quicktree_1.1 && make all CC="gcc -std=c99" touch lib/cleaned_old_protobuf_v003 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi libhandlegraph is root project or external_project -- Configuring done if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- The CXX compiler identification is GNU 11.3.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -- The C compiler identification is GNU 11.3.0 -- Detecting CXX compiler ABI info gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info ar rc cuTest.a *.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c ranlib cuTest.a gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Performing Test HAVE_CXA_DEMANGLE rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h -- Looking for C++ include cstdio - found [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o cp inc/stJson.h ../lib/stJson.h.tmp /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp mv ../lib/stJson.h.tmp ../lib/stJson.h -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp -- Configuring done [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp -- Generating done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-962s5Z/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[2]: 'bin/shuf' is up to date. In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/lib/libvw.* /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am rm -f /build/vg-962s5Z/vg-1.30.0+ds/include/vg.pb.h /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found -- The CXX compiler identification is GNU 11.3.0 -- Detecting CXX compiler ABI info [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: copying file 'acinclude.d/ltsugar.m4' [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") libtoolize: copying file 'acinclude.d/ltversion.m4' -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:343 ] Protobuf_USE_STATIC_LIBS = OFF [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp libtoolize: copying file 'acinclude.d/lt~obsolete.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rc /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:479 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:487 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:505 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:519 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.13+ds cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp -- Checking for module 'jansson' -- Found jansson, version 2.14 -- Configuring done -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 11%] Performing configure step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp Re-run cmake no build system arguments -- Configuring done -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 14%] Performing build step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 16%] Performing install step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/vg.proto cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:15: installing './compile' In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp yes checking for g++ option to enable C++11 features... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C none needed checking whether make supports the include directive... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp yes (GNU style) checking dependency style of g++... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp gcc3 checking how to run the C++ preprocessor... g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a g++ -E rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' checking build system type... [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for gcc option to enable C11 features... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= none needed checking whether gcc understands -c and -o together... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 yes checking dependency style of gcc... /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o gcc3 checking for a sed that does not truncate output... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o /usr/bin/ranlib libhandlegraph.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o checking for ld used by gcc... cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ok checking for sysroot... no checking for a working dd... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp yes checking for strings.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for sys/stat.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 26%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm yes checking if gcc static flag -static works... mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm yes checking if gcc supports -c -o file.o... mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 30%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include 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(cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... [ 33%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp no checking dynamic linker characteristics... mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' [ 35%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E [ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes [ 40%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 42%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... [100%] Linking CXX static library libsdsl.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /usr/bin/ranlib libsdsl.a yes checking if g++ supports -c -o file.o... [ 45%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... [100%] Built target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks yes checking for egrep... (cached) /bin/grep -E make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend checking for boostlib >= 1.0 (100000)... make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build yes make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' checking whether the Boost::Program_Options library is available... [100%] Built target sdsl make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake [ 47%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat 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The sdsl include files are located in '/build/vg-962s5Z/vg-1.30.0+ds/include'. The library files are located in '/build/vg-962s5Z/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-962s5Z/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-962s5Z/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c [ 50%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp yes ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm checking for exit in -lboost_program_options... [ 52%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I .//../sonLib/lib/ -c impl/*.c yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ [ 57%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 59%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 61%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp . ./source_me.sh && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-962s5Z/vg-1.30.0+ds/include:/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" make && cp lib/libbdsg.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-962s5Z/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 66%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 69%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 71%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o [ 76%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ config.status: creating libvw.pc [ 76%] Built target vgio g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-962s5Z/vg-1.30.0+ds/lib . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dbg.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... [ 78%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking whether make supports nested variables... yes checking whether the C++ compiler works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ no checking for suffix of object files... In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 80%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp yes checking if gcc supports -c -o file.o... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gcsa.cpp yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-962s5Z/vg-1.30.0+ds/lib GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp yes checking for egrep... (cached) /bin/grep -E checking whether the Boost::Program_Options library is available... /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for main in -lboost_program_options... [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c lcp.cpp PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c bwtmerge.cpp checking that generated files are newer than configure... done configure: creating ./config.status /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c fast_locate.cpp [ 90%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h [ 95%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake rm -f *.o rm -f *.lo /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwt.cpp make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/ranlib libvgio.a rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_graph.cpp Consolidate compiler generated dependencies of target vgio make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio_static make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp -- Set runtime path of "/build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include/vg -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:18: required from here /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_gbwt.cpp depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c benchmark.cpp In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src 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-I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall 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vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread 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-I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer 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-DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:27: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o bin/vg-ssse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" ./install.sh /build/vg-962s5Z/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-962s5Z/vg-1.30.0+ds/obj && cp src/*.h /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-962s5Z/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-962s5Z/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c Library will be installed in '/build/vg-962s5Z/vg-1.30.0+ds' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all rm -f /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* if [ ! -d obj ]; then mkdir -p obj; fi rm -Rf include/boost if [ ! -d lib ]; then mkdir -p lib; fi WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' touch lib/cleaned_old_boost find bin obj lib -type f -delete make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc cd quicktree_1.1 && make all CC="gcc -std=c99" make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -Rf include/google/protobuf deps/protobuf gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c if [ ! -d obj ]; then mkdir -p obj; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi touch lib/cleaned_old_protobuf_v003 if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi libhandlegraph is root project or external_project -- Configuring done CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' -- The CXX compiler identification is GNU 11.3.0 make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- The C compiler identification is GNU 11.3.0 -- Detecting CXX compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o ar rc cuTest.a *.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o gcc -std=c99 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -- Performing Test HAVE_CXA_DEMANGLE /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/structures' . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-962s5Z/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE g++ -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. cp inc/bioioC.h ../lib/bioioC.h.tmp -- Looking for C++ include cstdio mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp -- Looking for C++ include cstdio - found mv ../lib/jsmn.h.tmp ../lib/jsmn.h -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp -- Configuring done mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp -- Generating done mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/progress_bar' g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Make dest directory [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/lib/libvw.* /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./autogen.sh || true cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ./autogen.sh: 22: [[: not found cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: copying file 'acinclude.d/ltoptions.m4' [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:15: installing './compile' configure.ac:3: installing './missing' g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o cluster/Makefile.am: installing './depcomp' ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-962s5Z/vg-1.30.0+ds/include -L. -L/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o configure.ac:12: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:12: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:12: the top level configure.ac:15: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.ac:15: You should run autoupdate. acinclude.d/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.ac:15: the top level configure.ac:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:17: the top level configure.ac:24: warning: The macro `AC_LANG_C' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.d/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:24: the top level configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:44: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:44: the top level configure.ac:49: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:49: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:49: the top level configure.ac:55: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:55: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:61: the top level mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp ar rc /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp ranlib /build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-962s5Z/vg-1.30.0+ds/include/vg.pb.h /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-962s5Z/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes -- The CXX compiler identification is GNU 11.3.0 checking whether make supports nested variables... -- Detecting CXX compiler ABI info yes checking whether the C++ compiler works... -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp no checking for suffix of object files... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ o checking whether the compiler supports GNU C++... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp yes checking whether g++ accepts -g... -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:343 ] Protobuf_USE_STATIC_LIBS = OFF yes checking for g++ option to enable C++11 features... [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp gcc3 checking how to run the C++ preprocessor... -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:479 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:487 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:505 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.23/Modules/FindProtobuf.cmake:519 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.13+ds g++ -E -- Checking for module 'jansson' checking build system type... -- Found jansson, version 2.14 x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp none needed checking whether gcc understands -c and -o together... -- Configuring done yes checking dependency style of gcc... -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake gcc3 checking for a sed that does not truncate output... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean /bin/sed checking for grep that handles long lines and -e... make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake /bin/grep checking for egrep... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake /bin/grep -E checking for fgrep... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /bin/grep -F checking for ld used by gcc... /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... [ 2%] Creating directories for 'handlegraph' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend /usr/bin/cmake -P /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp/handlegraph-mkdirs.cmake make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 2%] Built target link_target [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... [ 7%] Running cpp protocol buffer compiler on deps/vg.proto 1572864 /usr/bin/protoc --cpp_out /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... [ 11%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o [ 16%] Performing configure step for 'handlegraph' /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... Re-run cmake no build system arguments -- Configuring done -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 19%] Performing build step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 ok checking for sysroot... no checking for a working dd... /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= checking for mt... no checking if : is a manifest tool... Dependencies file "CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o.d" is newer than depends file "/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target handlegraph_objs no make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' checking for stdio.h... make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= yes checking for stdlib.h... make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend yes checking for string.h... make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 21%] Performing install step for 'handlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install yes checking for inttypes.h... make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp yes checking for stdint.h... make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' yes checking for strings.h... [ 66%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' yes checking for sys/stat.h... [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake yes checking for sys/types.h... -- Install configuration: "" -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 28%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 28%] Built target handlegraph yes checking for unistd.h... [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp yes checking for dlfcn.h... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for objdir... .libs make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sonLib' make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' checking if gcc supports -fno-rtti -fno-exceptions... make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= [ 96%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-962s5Z/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-962s5Z/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-962s5Z/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/sonLib /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c /usr/bin/ranlib libhandlegraph.a yes checking if gcc static flag -static works... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_static [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libhandlegraph' ar rc 3EdgeConnected.a *.o yes checking if gcc supports -c -o file.o... ranlib 3EdgeConnected.a make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend rm *.o make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= mv 3EdgeConnected.a ../..//../sonLib/lib/ make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cp inc/*.h ../..//../sonLib/lib/ [ 35%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg.pb.cc gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I .//../sonLib/lib/ -c impl/*.c GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... 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[100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp yes checking for egrep... (cached) /bin/grep -E checking for boostlib >= 1.0 (100000)... gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-962s5Z/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking whether the Boost::Program_Options library is available... [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp yes In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [100%] Linking CXX static library libsdsl.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 yes checking for joinable pthread attribute... /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/ranlib libsdsl.a yes checking that generated files are newer than configure... done configure: creating ./config.status make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: 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/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-962s5Z/vg-1.30.0+ds/include'. The library files are located in '/build/vg-962s5Z/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gcsa.cpp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/pinchesAndCacti' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c lcp.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_graph.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ config.status: executing depfiles commands /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... [ 59%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:18: required from here /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... [ 66%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o yes checking for inttypes.h... /usr/bin/ranlib libvgio.a yes checking for stdint.h... make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' yes checking for strings.h... [ 66%] Built target vgio_static [ 69%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/edit.cpp yes checking if gcc supports -c -o file.o... [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' no checking dynamic linker characteristics... rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp . ./source_me.sh && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-962s5Z/vg-1.30.0+ds/include:/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" make && cp lib/libbdsg.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-962s5Z/vg-1.30.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... rm -r bin yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' checking how to run the C++ preprocessor... g++ -E g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:13: required from here /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking if g++ static flag -static works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c bwtmerge.cpp [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for egrep... (cached) /bin/grep -E checking whether the Boost::Program_Options library is available... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp yes checking for main in -lboost_program_options... In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/registry.cpp yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream.cpp yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:32: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dynamic_gbwt.cpp config.status: creating Makefile [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 config.status: creating vowpalwabbit/Makefile /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' config.status: executing libtool commands [100%] Built target vgio . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-962s5Z/vg-1.30.0+ds/lib" make make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio -B/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target vgio make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la Consolidate compiler generated dependencies of target vgio_static make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 Making clean in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' rm -f spanning_tree rm -rf .libs _libs rm -f *.o Install the project... rm -f ../vowpalwabbit/*.o /usr/bin/cmake -P cmake_install.cmake rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library -- Install configuration: "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict -- Set runtime path of "/build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include -- Up-to-date: /build/vg-962s5Z/vg-1.30.0+ds/include/vg -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake rm -rf .libs _libs make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libvgio' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:25: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c test.cpp depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_ri.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c benchmark.cpp depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c remove_seq.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ rm -f lib/libbdsg.a /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwtgraph.cpp depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa.cpp depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:12: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:26: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c minimizer.cpp depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_cover.cpp In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:28: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1535:18: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:28: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:40: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:35: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:20: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:28: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:25: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:19: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:16: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:21: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:27: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa2gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 parse_args.cc: In function ‘const char* VW::are_features_compatible(vw&, vw&)’: parse_args.cc:446:83: warning: expression does not compute the number of elements in this array; element type is ‘uint64_t’ {aka ‘long unsigned int’}, not ‘uint32_t’ {aka ‘unsigned int’} [-Wsizeof-array-div] 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ parse_args.cc:446:85: note: add parentheses around ‘sizeof (uint32_t)’ to silence this warning 446 | if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features)) | ^~~~~~~~~~~~~~~~ | ( ) In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:14: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:16: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:12: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:8: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:10: warning: ‘int ftime(timeb*)’ is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:10: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:16: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:23: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:33: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:19: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat 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-isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/memory:77, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/11/bits/shared_ptr.h:122:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 122 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:24: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:24: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-962s5Z/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-962s5Z/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-962s5Z/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-962s5Z/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-962s5Z/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:27: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o bin/vg-sse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' CXXFLAGS="-g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" CFLAGS="-g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" dh_auto_build -- SFX=-plain all test/build_graph bin/shuf make -j10 "INSTALL=install --strip-program=true" SFX=-plain all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/vg-962s5Z/vg-1.30.0+ds Library will be installed in '/build/vg-962s5Z/vg-1.30.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[2]: 'bin/shuf' is up to date. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 11.3.0 -- The C compiler identification is GNU 11.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done -- Build files have been written to: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Linking CXX static library libsdsl.a cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target sdsl make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-962s5Z/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-962s5Z/vg-1.30.0+ds/include'. The library files are located in '/build/vg-962s5Z/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-962s5Z/vg-1.30.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-962s5Z/vg-1.30.0+ds/lib . ./source_me.sh && rm -Rf /build/vg-962s5Z/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-962s5Z/vg-1.30.0+ds/include:/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/vg-962s5Z/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-962s5Z/vg-1.30.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-962s5Z/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gcsa2' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c bwtmerge.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c fast_locate.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-962s5Z/vg-1.30.0+ds/include -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-962s5Z/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-962s5Z/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-962s5Z/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-962s5Z/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-962s5Z/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-962s5Z/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds/deps/gbwtgraph' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:27: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-962s5Z/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-962s5Z/vg-1.30.0+ds/include -isystem /build/vg-962s5Z/vg-1.30.0+ds/include -I. -I/build/vg-962s5Z/vg-1.30.0+ds/src -I/build/vg-962s5Z/vg-1.30.0+ds/src/unittest -I/build/vg-962s5Z/vg-1.30.0+ds/src/subcommand -I/build/vg-962s5Z/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-962s5Z/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg-plain obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-962s5Z/vg-1.30.0+ds/lib /build/vg-962s5Z/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' cp bin/vg-plain debian/help/vg PATH=$PATH:/build/vg-962s5Z/vg-1.30.0+ds/debian/help \ help2man \ --no-discard-stderr \ --no-info \ --help-option=help \ --version-option=version \ --name='tools for working with genome variation graphs' \ vg > debian/vg.1 make[1]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_install debian/bin/simd-dispatch /usr/lib/vg/ dh_install bin/vg* usr/lib/vg/ mkdir -p /build/vg-962s5Z/vg-1.30.0+ds/debian/vg/usr/bin cd /build/vg-962s5Z/vg-1.30.0+ds/debian/vg/usr/bin \ && for prog in vg ; do \ ln -s ../lib/vg/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a dh_makeshlibs -a dh_shlibdeps -a objdump: Warning: Separate debug info file /usr/lib/x86_64-linux-gnu/libraptor2.so.0.0.0 found, but CRC does not match - ignoring dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-6), " make[1]: Leaving directory '/build/vg-962s5Z/vg-1.30.0+ds' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.30.0+ds-1+b2_amd64.deb'. dpkg-deb: building package 'vg' in '../vg_1.30.0+ds-1+b2_amd64.deb'. dpkg-genbuildinfo --build=any -O../vg_1.30.0+ds-1+b2_amd64.buildinfo dpkg-genchanges --build=any -O../vg_1.30.0+ds-1+b2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/vg-962s5Z /tmp/vg-1.30.0+ds-1+b2ltqxicg6 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.9litwyy3Qn... I: success in 7795.2511 seconds md5: Value of 'md5' differs for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb md5: Size differs for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb md5: Value of 'md5' differs for vg_1.30.0+ds-1+b2_amd64.deb md5: Size differs for vg_1.30.0+ds-1+b2_amd64.deb sha1: Value of 'sha1' differs for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb sha1: Size differs for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb sha1: Value of 'sha1' differs for vg_1.30.0+ds-1+b2_amd64.deb sha1: Size differs for vg_1.30.0+ds-1+b2_amd64.deb sha256: Value of 'sha256' differs for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb sha256: Size differs for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb sha256: Value of 'sha256' differs for vg_1.30.0+ds-1+b2_amd64.deb sha256: Size differs for vg_1.30.0+ds-1+b2_amd64.deb Checksums: FAIL Cannot generate diffoscope for vg-dbgsym_1.30.0+ds-1+b2_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/17b6c9533fca53efc71ef5e3b3f4ebf5d45f7ad2e3aa333e9b6d8f68497221cd/download Cannot generate diffoscope for vg_1.30.0+ds-1+b2_amd64.deb: RetryError[]