I: pbuilder: network access will be disabled during build I: Current time: Tue Mar 18 05:59:26 -12 2025 I: pbuilder-time-stamp: 1742320766 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [vg_1.59.0+ds-0.1.dsc] I: copying [./vg_1.59.0+ds.orig.tar.xz] I: copying [./vg_1.59.0+ds-0.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./vg_1.59.0+ds-0.1.dsc: unsupported subcommand dpkg-source: info: extracting vg in vg-1.59.0+ds dpkg-source: info: unpacking vg_1.59.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.59.0+ds-0.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying avoid_abs_confusion dpkg-source: info: applying gcc-12 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/430661/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='bb951dc55a42415e899fa6dee25e9632' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='430661' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2jjtNNm2/pbuilderrc_jcp2 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2jjtNNm2/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/430661/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pv, bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools, unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, tabix, xxd, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, libzstd-dev, doxygen, graphviz dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19898 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on pv; however: Package pv is not installed. pbuilder-satisfydepends-dummy depends on bsdextrautils | bsdmainutils; however: Package bsdextrautils is not installed. Package bsdmainutils is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on rs; however: Package rs is not installed. pbuilder-satisfydepends-dummy depends on libffi-dev; however: Package libffi-dev is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler is not installed. pbuilder-satisfydepends-dummy depends on libprotoc-dev; however: Package libprotoc-dev is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on libjansson-dev; however: Package libjansson-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on libtool; however: Package libtool is not installed. pbuilder-satisfydepends-dummy depends on jq; however: Package jq is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on unzip; however: Package unzip is not installed. pbuilder-satisfydepends-dummy depends on librdf0-dev; however: Package librdf0-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on gtk-doc-tools; however: Package gtk-doc-tools is not installed. pbuilder-satisfydepends-dummy depends on raptor2-utils; however: Package raptor2-utils is not installed. pbuilder-satisfydepends-dummy depends on rasqal-utils; however: Package rasqal-utils is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on gawk; however: Package gawk is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-dev is not installed. pbuilder-satisfydepends-dummy depends on libpixman-1-dev; however: Package libpixman-1-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libbackward-cpp-dev; however: Package libbackward-cpp-dev is not installed. pbuilder-satisfydepends-dummy depends on elfutils; however: Package elfutils is not installed. pbuilder-satisfydepends-dummy depends on libdw-dev; however: Package libdw-dev is not installed. pbuilder-satisfydepends-dummy depends on libelf-dev; however: Package libelf-dev is not installed. pbuilder-satisfydepends-dummy depends on libraptor2-dev; however: Package libraptor2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev; however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on fastahack; however: Package fastahack is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libtsl-hopscotch-map-dev; however: Package libtsl-hopscotch-map-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.1); however: Package libvcflib-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bison{a} bsdextrautils{a} bwa{a} ca-certificates{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} docbook-xml{a} docbook-xsl{a} doxygen{a} dwz{a} elfutils{a} fastahack{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} girepository-tools{a} graphviz{a} groff-base{a} gtk-doc-tools{a} help2man{a} icu-devtools{a} intltool-debian{a} jq{a} krb5-multidev{a} libabsl20240722{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libasm1t64{a} libavif16{a} libbackward-cpp-dev{a} libblas3{a} libblkid-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdw-dev{a} libdw1t64{a} libedit2{a} libelf-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfastahack-dev{a} libfastahack0{a} libffi-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfmt10{a} libfontconfig-dev{a} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgd3{a} libgfortran5{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice-dev{a} libice6{a} libicu-dev{a} libicu76{a} libidn2-0{a} libidn2-dev{a} libimagequant0{a} libjansson-dev{a} libjbig0{a} libjemalloc-dev{a} libjemalloc2{a} libjpeg62-turbo{a} libjq1{a} libjson-c5{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblab-gamut1{a} liblapack3{a} libldap-dev{a} libldap2{a} liblerc4{a} libllvm19{a} liblocale-gettext-perl{a} libltdl7{a} liblz4-dev{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libmhash2{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libonig5{a} libosp5{a} libp11-kit-dev{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpathplan4{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc-dev{a} libprotoc32t64{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraptor2-0{a} libraptor2-dev{a} libraqm0{a} librasqal3-dev{a} librasqal3t64{a} librav1e0.7{a} librdf0-dev{a} librdf0t64{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsigsegv2{a} libsimde-dev{a} libsm-dev{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libsparsehash-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libsvtav1enc2{a} libsysprof-capture-4-dev{a} libtabixpp-dev{a} libtabixpp0t64{a} libtasn1-6{a} libtasn1-6-dev{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtsl-hopscotch-map-dev{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib2{a} libwebp7{a} libwfa2-0{a} libwfa2-dev{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft2{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxslt1-dev{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libxxhash-dev{a} libyajl-dev{a} libyajl2{a} libyuv0{a} libz3-4{a} libzstd-dev{a} littler{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} nettle-dev{a} opensp{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} pv{a} python3{a} python3-lxml{a} python3-minimal{a} python3-packaging{a} python3-pygments{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} rapidjson-dev{a} raptor2-utils{a} rasqal-utils{a} readline-common{a} rs{a} samtools{a} sensible-utils{a} sgml-base{a} sgml-data{a} tabix{a} tzdata{a} ucf{a} unzip{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} xxd{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-liberation krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libgpg-error-l10n libgpm2 libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libtasn1-doc libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib r-base-dev r-cran-abind r-cran-bench r-cran-bit64 r-cran-blob r-cran-brio r-cran-callr r-cran-covr r-cran-crayon r-cran-dbi r-cran-diagrammer r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-evaluate r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-here r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-mvtnorm r-cran-nanotime r-cran-palmerpenguins r-cran-pkgbuild r-cran-pkgdown r-cran-pkgload r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-purrr r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-survival r-cran-svglite r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-units r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended redland-utils shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 384 newly installed, 0 to remove and 0 not upgraded. Need to get 255 MB of archives. After unpacking 1098 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 flex arm64 2.6.4-8.2+b4 [412 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 8 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 9 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0050 [42.7 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-2 [853 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.0-1 [92.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-2 [1995 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-2 [1888 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-2 [746 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-2 [28.1 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-2 [337 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-2 [103 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-2 [43.6 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 bc arm64 1.07.1-4+b1 [101 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 bison arm64 2:3.8.2+dfsg-1+b2 [1149 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 bwa arm64 0.7.18-1 [198 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-1 [2268 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-3 [9526 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.3+b1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.13.0~rc2-1 [347 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-1 [9912 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1+b1 [56.2 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 82 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 docbook all 4.5-11 [126 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libosp5 arm64 1.5.2-15.2 [922 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 opensp arm64 1.5.2-15.2 [442 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 docbook-to-man arm64 1:2.0.0-48 [71.1 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 docbook-xml all 4.5-13 [77.4 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-3 [23.3 MB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.7-3 [12.0 MB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.7-3 [6860 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2.1 [4519 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libdw1t64 arm64 0.192-4 [237 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libasm1t64 arm64 0.192-4 [28.2 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.13.0~rc2-1 [341 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libjson-c5 arm64 0.18+ds-1 [45.2 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libdebuginfod1t64 arm64 0.192-4 [31.3 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 elfutils arm64 0.192-4 [464 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b2 [4920 B] Get: 112 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 fastahack arm64 1.0.0+dfsg-11+b2 [12.2 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1.1 [274 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.1 [318 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.1 [387 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.1 [463 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 native-architecture all 0.2.6 [2264 B] Get: 122 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.0-2 [1424 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libgirepository-2.0-0 arm64 2.84.0-2 [132 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 girepository-tools arm64 2.84.0-2 [137 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-3 [39.2 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-3 [61.1 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.12.0-1 [1672 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libabsl20240722 arm64 20240722.0-1.5 [452 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-9+b1 [661 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1904.20250204-1 [137 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.2.0-1 [125 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.7-1 [11.5 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b3 [153 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.7-1 [15.1 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.7-1 [442 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-4 [415 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-1 [213 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [52.9 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [33.7 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-3 [41.2 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-3 [629 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-3 [181 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-3 [198 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-3 [572 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.2 [221 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.3.1-1+b1 [1139 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 xsltproc arm64 1.1.35-1.2 [115 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 gtk-doc-tools all 1.34.0-2 [328 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 76.1-3 [200 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libonig5 arm64 6.9.9-1+b1 [181 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libjq1 arm64 1.7.1-3+b1 [148 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 jq arm64 1.7.1-3+b1 [77.3 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 uuid-dev arm64 2.40.4-5 [48.5 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libblkid-dev arm64 2.40.4-5 [209 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.1+b2 [10.6 MB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1+b2 [332 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4.1+b2 [369 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 212 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.4-1+b1 [130 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libcairo-script-interpreter2 arm64 1.18.4-1+b1 [57.4 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.0-1 [144 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libpng-dev arm64 1.6.47-1.1 [360 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libfreetype-dev arm64 2.13.3+dfsg-1 [600 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libfontconfig-dev arm64 2.15.0-2.1 [412 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libffi-dev arm64 3.4.7-1 [57.1 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libsepol-dev arm64 3.8.1-1 [356 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libpcre2-16-0 arm64 10.45-1 [247 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libpcre2-32-0 arm64 10.45-1 [237 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libpcre2-posix3 arm64 10.45-1 [63.7 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libpcre2-dev arm64 10.45-1 [749 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libselinux1-dev arm64 3.8.1-1 [172 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libmount-dev arm64 2.40.4-5 [29.6 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libsysprof-capture-4-dev arm64 48.0-1 [49.7 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev arm64 2.84.0-2 [1706 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 libglib2.0-data all 2.84.0-2 [1286 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libglib2.0-bin arm64 2.84.0-2 [124 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev-bin arm64 2.84.0-2 [163 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev-bin arm64 2.84.0-2 [52.9 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev arm64 2.84.0-2 [53.6 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libpixman-1-dev arm64 0.44.0-3 [11.4 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 242 http://deb.debian.org/debian unstable/main arm64 libice-dev arm64 2:1.1.1-1 [73.0 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libsm-dev arm64 2:1.2.4-1 [38.0 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.11-1 [23.9 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.5-1 [44.2 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-2+b1 [182 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libx11-dev arm64 2:1.8.10-2 [877 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libxcb-render0-dev arm64 1.17.0-2+b1 [119 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0-dev arm64 1.17.0-2+b1 [108 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libxext-dev arm64 2:1.3.4-1+b3 [105 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libxrender-dev arm64 1:0.9.10-1.1+b4 [35.7 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libcairo2-dev arm64 1.18.4-1+b1 [43.4 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.8-2 [101 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-2 [305 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.8.0-1 [89.4 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.11.0-1 [33.9 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.11.0-1 [174 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.7+dfsg-1 [335 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.13.0~rc2-1 [473 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4+b2 [4888 B] Get: 279 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libelf-dev arm64 0.192-4 [94.9 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.4-1 [319 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libdw-dev arm64 0.192-4 [320 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libfml0 arm64 0.1+git20221215.85f159e-1 [65.6 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libfml-dev arm64 0.1+git20221215.85f159e-1 [79.9 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.21+ds-1 [426 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.21+ds-1 [1658 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 76.1-3 [10.6 MB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libjansson-dev arm64 2.14-2+b3 [43.6 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libjemalloc2 arm64 5.3.0-3 [216 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libjemalloc-dev arm64 5.3.0-3 [356 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libxxhash-dev arm64 0.8.3-2 [82.6 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 liblz4-dev arm64 1.10.0-4 [85.1 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libmhash2 arm64 0.9.9.9-10 [94.5 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5+20250216-2 [340 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b1 [16.6 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b1 [16.3 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libprotobuf32t64 arm64 3.21.12-10+b6 [859 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b6 [250 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libprotobuf-dev arm64 3.21.12-10+b6 [1263 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libprotoc32t64 arm64 3.21.12-10+b6 [790 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libprotoc-dev arm64 3.21.12-10+b6 [937 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libyajl2 arm64 2.1.0-5+b2 [22.5 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libraptor2-0 arm64 2.0.16-5+b1 [164 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.3+b1 [751 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libxslt1-dev arm64 1.1.35-1.2 [345 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libyajl-dev arm64 2.1.0-5+b2 [31.0 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libraptor2-dev arm64 2.0.16-5+b1 [205 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 librasqal3t64 arm64 0.9.33-2.1+b2 [178 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 librasqal3-dev arm64 0.9.33-2.1+b2 [224 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 librdf0t64 arm64 1.0.17-4+b1 [100 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 librdf0-dev arm64 1.0.17-4+b1 [239 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b2 [32.4 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b2 [37.9 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libssw0 arm64 1.1-15+b2 [20.0 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 libssw-dev arm64 1.1-15+b2 [23.4 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libtabixpp0t64 arm64 1.1.2-2.1+b1 [9504 B] Get: 325 http://deb.debian.org/debian unstable/main arm64 libtabixpp-dev arm64 1.1.2-2.1+b1 [9052 B] Get: 326 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.6+ds-1 [79.1 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libwfa2-0 arm64 2.3.3-4+b2 [55.1 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libvcflib2 arm64 1.0.12+dfsg-1 [199 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libwfa2-dev arm64 2.3.3-4+b2 [74.8 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libvcflib-dev arm64 1.0.12+dfsg-1 [77.8 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-29 [163 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.3-1+b1 [28.1 MB] Get: 341 http://deb.debian.org/debian unstable/main arm64 r-cran-littler arm64 0.3.20-2 [102 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 littler all 0.3.20-2 [16.0 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 r-cran-rcpp arm64 1.0.14-1 [2062 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 r-cran-plyr arm64 1.8.9-1+b1 [791 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 r-cran-cli arm64 3.6.4-1 [1368 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 r-cran-glue arm64 1.8.0-1 [165 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 r-cran-rlang arm64 1.1.5-1 [1706 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 r-cran-isoband arm64 0.2.7-1+b1 [1614 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 r-cran-mass arm64 7.3-65-1 [1112 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 r-cran-lattice arm64 0.22-6-1+b1 [1417 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 r-cran-nlme arm64 3.1.167-1 [2327 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 r-cran-matrix arm64 1.7-3-1 [3934 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 r-cran-mgcv arm64 1.9-1-1+b1 [3218 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 r-cran-farver arm64 2.1.2-1+b1 [1397 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1713 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 r-cran-r6 all 2.6.1-1 [106 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 r-cran-scales all 1.3.0-1 [677 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 r-cran-fansi arm64 1.0.6-1 [626 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 r-cran-magrittr arm64 2.0.3-1+b1 [203 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 r-cran-utf8 arm64 1.2.4-1+b1 [133 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 r-cran-vctrs arm64 0.6.5-1+b1 [1378 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [425 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 libvcflib-tools arm64 1.0.12+dfsg-1 [548 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 protobuf-compiler arm64 3.21.12-10+b6 [84.9 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 pv arm64 1.9.31-1 [111 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 379 http://deb.debian.org/debian unstable/main arm64 raptor2-utils arm64 2.0.16-5+b1 [34.7 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 rasqal-utils arm64 0.9.33-2.1+b2 [43.1 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 rs arm64 20200313-1+b1 [15.2 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.21-1 [637 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 tabix arm64 1.21+ds-1 [461 kB] Get: 384 http://deb.debian.org/debian unstable/main arm64 xxd arm64 2:9.1.1113-1 [98.2 kB] Fetched 255 MB in 3s (93.1 MB/s) Preconfiguring packages ... Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-7_arm64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b4_arm64.deb ... Unpacking flex (2.6.4-8.2+b4) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-6_all.deb ... 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Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:arm64 (1.11.0-1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.6-1) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libcdt5:arm64 (2.42.4-3) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libcgraph6:arm64 (2.42.4-3) ... Setting up libicu76:arm64 (76.1-3) ... Setting up libpaper2:arm64 (2.2.5-0.3+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libprotoc32t64:arm64 (3.21.12-10+b6) ... Setting up libde265-0:arm64 (1.0.15-1+b3) ... Setting up libdivsufsort3:arm64 (2.0.1-6+b1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up openssl (3.4.1-1) ... Setting up libdeflate-dev:arm64 (1.23-1+b1) ... Setting up tabix (1.21+ds-1) ... Setting up libyuv0:arm64 (0.0.1904.20250204-1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-2) ... Setting up libssw0:arm64 (1.1-15+b2) ... Setting up libjson-c5:arm64 (0.18+ds-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-2) ... Setting up libjansson-dev:arm64 (2.14-2+b3) ... Setting up libonig5:arm64 (6.9.9-1+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libfmt10:arm64 (10.1.1+ds1-4) ... Setting up libpython3-stdlib:arm64 (3.13.2-2) ... Setting up libdivsufsort-dev:arm64 (2.0.1-6+b1) ... Setting up rs (20200313-1+b1) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libblkid-dev:arm64 (2.40.4-5) ... Setting up libllvm19:arm64 (1:19.1.7-3) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libavif16:arm64 (1.2.0-1) ... Setting up flex (2.6.4-8.2+b4) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5+20250216-2) ... Setting up gettext (0.23.1-1) ... Setting up libfml-dev:arm64 (0.1+git20221215.85f159e-1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up libclang1-19 (1:19.1.7-3) ... Setting up libxau-dev:arm64 (1:1.0.11-1) ... Setting up libxpm4:arm64 (1:3.5.17-1+b3) ... Setting up libpcre2-dev:arm64 (10.45-1) ... Setting up protobuf-compiler (3.21.12-10+b6) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ... Setting up libice-dev:arm64 (2:1.1.1-1) ... Setting up libssw-dev:arm64 (1.1-15+b2) ... Setting up libtool (2.5.4-4) ... Setting up python3.13 (3.13.2-2) ... Setting up libselinux1-dev:arm64 (3.8.1-1) ... Setting up libjq1:arm64 (1.7.1-3+b1) ... Setting up fontconfig-config (2.15.0-2.1) ... Setting up libpng-dev:arm64 (1.6.47-1.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up fastahack (1.0.0+dfsg-11+b2) ... Setting up python3 (3.13.2-2) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up libpaper-utils (2.2.5-0.3+b1) ... Setting up opensp (1.5.2-15.2) ... Setting up libngtcp2-dev:arm64 (1.11.0-1) ... Setting up libffi-dev:arm64 (3.4.7-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:arm64 (3.21.12-10+b6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libxdmcp-dev:arm64 (1:1.1.5-1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up libglib2.0-0t64:arm64 (2.84.0-2) ... No schema files found: doing nothing. Setting up python3-packaging (24.2-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libelf-dev:arm64 (0.192-4) ... Setting up icu-devtools (76.1-3) ... Setting up liblz4-dev:arm64 (1.10.0-4) ... Setting up libsmithwaterman-dev:arm64 (0.0+git20160702.2610e25-12+b2) ... Setting up ucf (3.0050) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.8-2) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgvpr2:arm64 (2.42.4-3) ... Setting up libprotoc-dev:arm64 (3.21.12-10+b6) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up jq (1.7.1-3+b1) ... Setting up libxslt1.1:arm64 (1.1.35-1.2) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2.1) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libicu-dev:arm64 (76.1-3) ... Setting up libmount-dev:arm64 (2.40.4-5) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libclang-cpp19 (1:19.1.7-3) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up fontconfig (2.15.0-2.1) ... Regenerating fonts cache... done. Setting up libgio-2.0-dev-bin (2.84.0-2) ... Setting up libxft2:arm64 (2.3.6-1+b4) ... Setting up libgio-2.0-dev:arm64 (2.84.0-2) ... Setting up libxcb1-dev:arm64 (1.17.0-2+b1) ... Setting up libdebuginfod-common (0.192-4) ... Setting up libtirpc3t64:arm64 (1.3.6+ds-1) ... Setting up libgirepository-2.0-0:arm64 (2.84.0-2) ... Setting up libsm-dev:arm64 (2:1.2.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libpango-1.0-0:arm64 (1.56.3-1) ... Setting up xsltproc (1.1.35-1.2) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libx11-dev:arm64 (2:1.8.10-2) ... Setting up libglib2.0-bin (2.84.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libdw-dev:arm64 (0.192-4) ... Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libfreetype-dev:arm64 (2.13.3+dfsg-1) ... Setting up libxcb-shm0-dev:arm64 (1.17.0-2+b1) ... Setting up libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Setting up doxygen (1.9.8+ds-2.1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-5) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libxcb-render0-dev:arm64 (1.17.0-2+b1) ... Setting up libxext-dev:arm64 (2:1.3.4-1+b3) ... Setting up python3-lxml:arm64 (5.3.1-1+b1) ... Setting up libcairo-gobject2:arm64 (1.18.4-1+b1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... Setting up libxrender-dev:arm64 (1:0.9.10-1.1+b4) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-5) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up libcairo-script-interpreter2:arm64 (1.18.4-1+b1) ... Setting up libxmu6:arm64 (2:1.1.3-3+b4) ... Setting up girepository-tools:arm64 (2.84.0-2) ... Setting up libxslt1-dev:arm64 (1.1.35-1.2) ... Setting up libcurl4t64:arm64 (8.13.0~rc2-1) ... Setting up libkdb5-10t64:arm64 (1.21.3-5) ... Setting up libfontconfig-dev:arm64 (2.15.0-2.1) ... Setting up libraptor2-0:arm64 (2.0.16-5+b1) ... Setting up raptor2-utils (2.0.16-5+b1) ... Setting up libcurl3t64-gnutls:arm64 (8.13.0~rc2-1) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.11.0-1) ... Setting up librasqal3t64:arm64 (0.9.33-2.1+b2) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up librdf0t64:arm64 (1.0.17-4+b1) ... Setting up r-base-core (4.4.3-1+b1) ... Creating config file /etc/R/Renviron with new version Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1+b1) ... Setting up r-cran-nlme (3.1.167-1) ... Setting up r-cran-farver (2.1.2-1+b1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-5) ... Setting up cmake (3.31.6-1) ... Setting up libhts3t64:arm64 (1.21+ds-1) ... Setting up r-cran-r6 (2.6.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1+b1) ... Setting up krb5-multidev:arm64 (1.21.3-5) ... Setting up r-cran-littler (0.3.20-2) ... Setting up libglib2.0-dev-bin (2.84.0-2) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up rasqal-utils (0.9.33-2.1+b2) ... Setting up libdebuginfod1t64:arm64 (0.192-4) ... Setting up r-cran-rlang (1.1.5-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-fansi (1.0.6-1) ... Setting up r-cran-mass (7.3-65-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.4-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.21-1) ... Setting up libkrb5-dev:arm64 (1.21.3-5) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1+b1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libglib2.0-dev:arm64 (2.84.0-2) ... Setting up r-cran-plyr (1.8.9-1+b1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1+b1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-3-1) ... Setting up r-cran-mgcv (1.9-1-1+b1) ... Setting up libtabixpp0t64:arm64 (1.1.2-2.1+b1) ... Setting up libcairo2-dev:arm64 (1.18.4-1+b1) ... Setting up r-cran-vctrs (0.6.5-1+b1) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up elfutils (0.192-4) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up libcurl4-gnutls-dev:arm64 (8.13.0~rc2-1) ... Setting up libvcflib2:arm64 (1.0.12+dfsg-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up libraptor2-dev:arm64 (2.0.16-5+b1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libhts-dev:arm64 (1.21+ds-1) ... Setting up librasqal3-dev (0.9.33-2.1+b2) ... Setting up libvcflib-tools (1.0.12+dfsg-1) ... Setting up librdf0-dev (1.0.17-4+b1) ... Setting up libtabixpp-dev:arm64 (1.1.2-2.1+b1) ... Setting up libvcflib-dev:arm64 (1.0.12+dfsg-1) ... Setting up libheif-plugin-dav1d:arm64 (1.19.7-1) ... Setting up libheif-plugin-libde265:arm64 (1.19.7-1) ... Setting up libheif1:arm64 (1.19.7-1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-3) ... Setting up graphviz (2.42.4-3) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-7) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-13) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-48) ... Setting up gtk-doc-tools (1.34.0-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/vg-1.59.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../vg_1.59.0+ds-0.1_source.changes dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.59.0+ds-0.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' find /build/reproducible-path/vg-1.59.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j12 clean make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -rf ../bin ../lib cd cutest && make clean make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_clean: error: make -j12 clean returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_autoreconf --sourcedirectory=/build/reproducible-path/vg-1.59.0+ds/deps/vowpal_wabbit make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_configure debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/help find . -type d -name simde | xargs rm -Rf dh_auto_build -- all test/build_graph bin/shuf make -j12 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. cp -r deps/sparsepp/sparsepp include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. rm -Rf include/google/protobuf deps/protobuf gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ touch lib/cleaned_old_protobuf_v003 touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi -- The C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o -- The CXX compiler identification is GNU 14.2.0 gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -- Detecting C compiler ABI info - done gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info - done -- Configuring done (1.7s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG libhandlegraph is root project or external_project -- Configuring done (1.8s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h -- Performing Test HAVE_CXA_DEMANGLE cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -I inc -I ../lib/ -c impl/*.c -- Looking for C++ include cstdio - found cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (5.5s) src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -- Generating done (0.3s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 [ 31%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp [ 40%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:806:75: note: declared here 806 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:814:68: note: declared here 814 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:815:68: note: declared here 815 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp [ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp [ 33%] Linking CXX static library libkff.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Built target kff [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o [ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 68%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp [ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o [ 66%] Linking CXX executable kff_example /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 66%] Built target kff_example [ 83%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 1 [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [100%] Built target reader_bench make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:550:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 ranlib sonLib.a rm *.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file=CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j12 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:39: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make: *** [debian/rules:22: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/430661 and its subdirectories