I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 29 08:36:29 -12 2025 I: pbuilder-time-stamp: 1767040589 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [freebayes_1.3.7-1~exp.dsc] I: copying [./freebayes_1.3.7.orig.tar.gz] I: copying [./freebayes_1.3.7-1~exp.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Mar 9 10:23:15 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./freebayes_1.3.7-1~exp.dsc: no acceptable signature found dpkg-source: info: extracting freebayes in freebayes-1.3.7 dpkg-source: info: unpacking freebayes_1.3.7.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.7-1~exp.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2765857/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f26b98e2c4c94979b18aca63ed588203' 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='2765857' 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.XqQj8OYE/pbuilderrc_FjDx --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XqQj8OYE/b1 --logfile b1/build.log freebayes_1.3.7-1~exp.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2765857/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: amd64 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), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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 meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on ninja-build; however: Package ninja-build is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.0~rc2+dfsg-3~); however: Package libvcflib-dev is not installed. pbuilder-satisfydepends-dummy depends on libtabixpp-dev; however: Package libtabixpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqlib-dev (>= 1.1.2+dfsg-5); however: Package libseqlib-dev is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} bsdextrautils{a} ca-certificates{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbwa-dev{a} libbz2-dev{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libharfbuzz0b{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-dev{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{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} libnsl2{a} libp11-kit-dev{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib-dev{a} libseqlib2{a} libsharpyuv0{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libtabixpp-dev{a} libtabixpp0t64{a} libtasn1-6-dev{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunbound8{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib2{a} libwebp7{a} libwfa2-0{a} libwfa2-dev{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6t64{a} libzstd-dev{a} littler{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} nettle-dev{a} ninja-build{a} openssl{a} parallel{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-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} readline-common{a} samtools{a} sensible-utils{a} sysstat{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bcron bzip2-doc cron cronie curl krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libtasn1-doc libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-base-dev r-cran-abind r-cran-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics 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-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-mvtnorm r-cran-pkgdown r-cran-png r-cran-processx r-cran-profvis r-cran-ps 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-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer 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 shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 240 newly installed, 0 to remove and 0 not upgraded. Need to get 132 MB of archives. After unpacking 348 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.1-1+b1 [54.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1+b1 [87.2 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1 [472 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b2 [4912 B] Get: 133 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b2 [27.9 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b2 [70.3 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b2 [82.0 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libjsoncpp-dev amd64 1.9.6-3 [25.0 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 162 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b1 [21.8 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b2 [172 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b1 [24.6 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libseqlib-dev amd64 1.2.0+dfsg-11+b2 [221 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b2 [41.4 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libtabixpp-dev amd64 1.1.2-2.1+b1 [9528 B] Get: 174 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4+b1 [61.1 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b2 [194 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libwfa2-dev amd64 2.3.3-4+b1 [79.7 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libvcflib-dev amd64 1.0.9+dfsg1-3+b2 [77.8 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 189 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-1 [16.0 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b2 [660 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 ninja-build amd64 1.12.1-1 [142 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 meson all 1.6.0-1 [628 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Fetched 132 MB in 4s (32.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19965 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20285 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... 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Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libfml-dev:amd64 (0.1+git20190320.b499514-1+b2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libssw-dev:amd64 (1.1-15+b1) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libldap-dev:amd64 (2.5.18+dfsg-3+b1) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-6+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up libsmithwaterman-dev:amd64 (0.0+git20160702.2610e25-12+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up bc (1.07.1-4) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up parallel (20240222+ds-2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... 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Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b2) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Setting up libseqlib-dev:amd64 (1.2.0+dfsg-11+b2) ... Setting up meson (1.6.0-1) ... Setting up libvcflib-tools (1.0.9+dfsg1-3+b2) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1+b1) ... Setting up libvcflib-dev:amd64 (1.0.9+dfsg1-3+b2) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... 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/freebayes-1.3.7/ && 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 > ../freebayes_1.3.7-1~exp_source.changes dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.7-1~exp dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson --builddir=build dh_auto_clean -O--buildsystem=meson -O--builddir=build dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build dh_clean -O--buildsystem=meson -O--builddir=build debian/rules binary dh binary --buildsystem=meson --builddir=build dh_update_autotools_config -O--buildsystem=meson -O--builddir=build dh_autoreconf -O--buildsystem=meson -O--builddir=build dh_auto_configure -O--buildsystem=meson -O--builddir=build cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.6.0 Source dir: /build/reproducible-path/freebayes-1.3.7 Build dir: /build/reproducible-path/freebayes-1.3.7/build Build type: native build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: cc (gcc 14.2.0 "cc (Debian 14.2.0-8) 14.2.0") C linker for the host machine: cc ld.bfd 2.43.1 C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-8) 14.2.0") C++ linker for the host machine: c++ ld.bfd 2.43.1 Host machine cpu family: x86_64 Host machine cpu: x86_64 Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency zlib found: YES 1.3.1 Run-time dependency liblzma found: YES 5.6.3 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.20 Library tabixpp found: YES Run-time dependency libvcflib found: YES 1.0 Run-time dependency libseqlib found: YES 1.0 Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/bin/prove) Build targets in project: 3 freebayes 1.3.6 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir : /var prefix : /usr python.bytecompile: -1 sysconfdir : /etc wrap_mode : nodownload Found ninja-1.12.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j42 -v [1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp [9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp [10/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp [12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp In file included from ../src/AlleleParser.h:32, from ../src/ResultData.h:10, from ../src/Marginals.h:7, from ../src/Marginals.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ../src/Marginals.h:4: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp ../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSequence(std::string)’: ../src/FBFasta.cpp:273:20: warning: pointer ‘pbegin’ used after ‘void free(void*)’ [-Wuse-after-free] 273 | s.resize((pend - pbegin)/sizeof(char)); | ~~~~~^~~~~~~~ ../src/FBFasta.cpp:272:9: note: call to ‘void free(void*)’ here 272 | free(seq); | ~~~~^~~~~ ../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSubSequence(std::string, int, int)’: ../src/FBFasta.cpp:316:20: warning: pointer ‘pbegin’ used after ‘void free(void*)’ [-Wuse-after-free] 316 | s.resize((pend - pbegin)/sizeof(char)); | ~~~~~^~~~~~~~ ../src/FBFasta.cpp:315:9: note: call to ‘void free(void*)’ here 315 | free(seq); | ~~~~^~~~~ [17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp [18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp In file included from ../src/AlleleParser.h:32, from ../src/DataLikelihood.h:20, from ../src/DataLikelihood.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../src/DataLikelihood.h:4: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../src/DataLikelihood.cpp:3: /usr/include/vcflib/multipermute.h:47:19: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 47 | ListElement() { } | ^ /usr/include/vcflib/multipermute.h:47:19: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:49:20: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 49 | ListElement(T val, ListElement* n) { | ^ /usr/include/vcflib/multipermute.h:49:20: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:64:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 64 | ~ListElement() { | ^ /usr/include/vcflib/multipermute.h:64:5: note: remove the ‘< >’ [20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp [21/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp In file included from ../src/AlleleParser.h:32, from ../src/freebayes.cpp:29: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../src/freebayes.cpp:9: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../src/freebayes.cpp:34: /usr/include/vcflib/multipermute.h:47:19: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 47 | ListElement() { } | ^ /usr/include/vcflib/multipermute.h:47:19: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:49:20: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 49 | ListElement(T val, ListElement* n) { | ^ /usr/include/vcflib/multipermute.h:49:20: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:64:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 64 | ~ListElement() { | ^ /usr/include/vcflib/multipermute.h:64:5: note: remove the ‘< >’ [22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp In file included from ../src/Genotype.cpp:3: /usr/include/vcflib/multipermute.h:47:19: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 47 | ListElement() { } | ^ /usr/include/vcflib/multipermute.h:47:19: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:49:20: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 49 | ListElement(T val, ListElement* n) { | ^ /usr/include/vcflib/multipermute.h:49:20: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:64:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 64 | ~ListElement() { | ^ /usr/include/vcflib/multipermute.h:64:5: note: remove the ‘< >’ [23/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp In file included from ../src/AlleleParser.h:32, from ../src/ResultData.h:10, from ../src/ResultData.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ../src/ResultData.h:4: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp In file included from ../src/AlleleParser.h:32, from ../src/AlleleParser.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../src/AlleleParser.h:4: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../src/AlleleParser.cpp:6: /usr/include/vcflib/multipermute.h:47:19: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 47 | ListElement() { } | ^ /usr/include/vcflib/multipermute.h:47:19: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:49:20: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 49 | ListElement(T val, ListElement* n) { | ^ /usr/include/vcflib/multipermute.h:49:20: note: remove the ‘< >’ /usr/include/vcflib/multipermute.h:64:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 64 | ~ListElement() { | ^ /usr/include/vcflib/multipermute.h:64:5: note: remove the ‘< >’ [25/27] rm -f libfreebayes_common.a && gcc-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libvcflib.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/x86_64-linux-gnu/libtabixpp.so -Wl,--end-group [27/27] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libtabixpp.so /usr/lib/x86_64-linux-gnu/libvcflib.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/freebayes-1.3.7' mkdir -p test/bash-tap/ ln -s -t test/bash-tap /build/reproducible-path/freebayes-1.3.7/debian/bash-tap/* mkdir -p test/test-simple-bash ln -s -t test/test-simple-bash /build/reproducible-path/freebayes-1.3.7/debian/test-simple-bash/* dh_auto_test -- -v --timeout-multiplier 100 cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=42 meson test -v --timeout-multiplier 100 ninja: Entering directory `/build/reproducible-path/freebayes-1.3.7/build' ninja: no work to do. 1/5 T00 RUNNING >>> MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=42 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t 2/5 T01 RUNNING >>> MALLOC_PERTURB_=137 MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01_call_variants.t 3/5 T01b RUNNING >>> MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=198 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01b_call_variants.t 4/5 T02 RUNNING >>> MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=177 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/02_multi_bam.t 5/5 T03 RUNNING >>> MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=93 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/03_reference_bases.t 5/5 T03 FAIL 2.42s exit status 1 ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/03_reference_bases.t .. 1..3 ok 1 - freebayes rejects invalid reference not ok 2 - freebayes does not put uppercase IUPAC bases in VCFs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 14 . A G # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA # ref 29 . C G # ref 31 . A T' not ok 3 - freebayes does not put lowercase IUPAC bases in VCFs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 14 . A G # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA # ref 29 . C G # ref 31 . A T' Failed 2/3 subtests Test Summary Report ------------------- t/03_reference_bases.t (Wstat: 0 Tests: 3 Failed: 2) Failed tests: 2-3 Files=1, Tests=3, 2 wallclock secs ( 0.04 usr 1.91 sys + 0.06 cusr 0.07 csys = 2.08 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 1/5 T00 FAIL 2.74s exit status 1 ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/00_region_and_target_handling.t .. 1..12 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty not ok 3 - ref:5-6 ref:7-8 not ok 4 - ref:5 ref:7 not ok 5 - ref:5- not ok 6 - full output not ok 7 - --targets t/../00_region_and_target_handling.t.bed not ok 8 - --region ref not ok 9 - ref:1,0- not ok 10 - ref:1,0-1,1 not ok 11 - ref:0-1 ok 12 - region outside of bounds error Failed 9/12 subtests Test Summary Report ------------------- t/00_region_and_target_handling.t (Wstat: 0 Tests: 12 Failed: 9) Failed tests: 3-11 Files=1, Tests=12, 2 wallclock secs ( 0.04 usr 0.02 sys + 1.36 cusr 0.14 csys = 1.56 CPU) Result: FAIL stderr: /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:5-6 ref:7-8' # at t/00_region_and_target_handling.t line 101. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:5 ref:7' # at t/00_region_and_target_handling.t line 104. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:5-' # at t/00_region_and_target_handling.t line 113. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'full output' # at t/00_region_and_target_handling.t line 124. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test '--targets t/../00_region_and_target_handling.t.bed' # at t/00_region_and_target_handling.t line 127. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test '--region ref' # at t/00_region_and_target_handling.t line 130. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:1,0-' # at t/00_region_and_target_handling.t line 138. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:1,0-1,1' # at t/00_region_and_target_handling.t line 141. # Failed test 'ref:0-1' # at t/00_region_and_target_handling.t line 145. Output: /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 4/5 T02 FAIL 3.18s exit status 1 ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/02_multi_bam.t .. 1..7 not ok 1 - freebayes calls from two identical BAMs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' not ok 2 - freebayes calls from two BAMs with different samples for different read groups # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' not ok 3 - freebayes calls from two BAMs with different technologies for different read groups # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups not ok 6 - freebayes calls multiple alts from two different BAMs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A C,G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' ok 7 - freebayes rejects two BAMs with the same name Failed 4/7 subtests Test Summary Report ------------------- t/02_multi_bam.t (Wstat: 0 Tests: 7 Failed: 4) Failed tests: 1-3, 6 Files=1, Tests=7, 3 wallclock secs ( 1.93 usr 0.01 sys + 0.20 cusr 0.25 csys = 2.39 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 2/5 T01 FAIL 3.85s exit status 1 ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/01_call_variants.t .. 1..16 not ok 1 - variant calling recovers most of the GiAB variants in a test region # got: '0' # expected: '1' ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference not ok 5 - freebayes processes all alignments in BAM input # got: '3333' # expected: '51' ok 6 - freebayes processes all alignments in CRAM input not ok 7 - freebayes correctly handles variant input # got: '0' # expected: '16' not ok 8 - freebayes puts required variants in output # got: '0' # expected: '3' not ok 9 - freebayes limits calls to input variants correctly # got: '0' # expected: '3' not ok 10 - freebayes reports all input variants even when there is no input data # got: '0' # expected: '16' not ok 11 - freebayes handles region and variant input # got: '0' # expected: '2' not ok 12 - freebayes limits to variant input correctly when region is given # got: '0' # expected: '2' not ok 13 - freebayes handles variant input and reading from stdin # got: '0' # expected: '3' not ok 14 - freebayes limits to variant input when reading from stdin # got: '0' # expected: '3' not ok 15 - freebayes handles region, stdin, and variant input # got: '0' # expected: '2' ok 16 - ! Failed 11/16 subtests Test Summary Report ------------------- t/01_call_variants.t (Wstat: 0 Tests: 16 Failed: 11) Failed tests: 1, 5, 7-15 Files=1, Tests=16, 4 wallclock secs ( 0.06 usr 0.02 sys + 0.73 cusr 2.31 csys = 3.12 CPU) Result: FAIL stderr: /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. t/01_call_variants.t: line 107: 2781630 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 3/5 T01b FAIL 4.44s exit status 1 ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/01b_call_variants.t .. 1..10 ok 1 - running in parallel makes no difference ok 2 - freebayes handles spaces in file names not ok 3 - freebayes handles region and variant input even with : in contig names # got: '0' # expected: '2' not ok 4 - freebayes can handle spliced reads # got: '0' # expected: '3' not ok 5 - freebayes produces the expected number of lines of gVCF output # got: '0' # expected: '20' not ok 6 - freebayes produces the expected number of lines of gVCF output # got: '3' # expected: '250' not ok 7 - freebayes produces the expected number of lines of gVCF output # got: '176' # expected: '12250' not ok 8 - the CNV map may be used to specify per-sample copy numbers # got: '0' # expected: '19' not ok 9 - freebayes makes the expected number of calls when capping coverage # got: '0' # expected: '22' not ok 10 - freebayes correctly uses CNV map with multiple entries # got: '0:0' # expected: '0:19' Failed 8/10 subtests Test Summary Report ------------------- t/01b_call_variants.t (Wstat: 0 Tests: 10 Failed: 8) Failed tests: 3-10 Files=1, Tests=10, 2 wallclock secs ( 0.05 usr 0.01 sys + 1.06 cusr 0.54 csys = 1.66 CPU) Result: FAIL stderr: /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― Summary of Failures: 5/5 T03 FAIL 2.42s exit status 1 1/5 T00 FAIL 2.74s exit status 1 4/5 T02 FAIL 3.18s exit status 1 2/5 T01 FAIL 3.85s exit status 1 3/5 T01b FAIL 4.44s exit status 1 Ok: 0 Expected Fail: 0 Fail: 5 Unexpected Pass: 0 Skipped: 0 Timeout: 0 Full log written to /build/reproducible-path/freebayes-1.3.7/build/meson-logs/testlog.txt cd build && tail -v -n \+0 meson-logs/testlog.txt ==> meson-logs/testlog.txt <== Log of Meson test suite run on 2025-12-29T08:40:16.206172 Inherited environment: DEB_HOST_MULTIARCH=x86_64-linux-gnu LC_ALL=C.UTF-8 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_LIBC=gnu FFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' SUDO_UID=105 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_GNU_SYSTEM=linux-gnu CFLAGS_FOR_BUILD='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCXXFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' DEB_BUILD_ARCH_BITS=64 DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DEB_HOST_ARCH=amd64 LDFLAGS_FOR_BUILD='-Wl,-z,relro -Wl,-z,now' DEB_TARGET_ARCH_ENDIAN=little PWD=/build/reproducible-path/freebayes-1.3.7 SOURCE_DATE_EPOCH=1678357078 MAIL=/var/mail/root OBJCFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OLDPWD=/ PBUILDER_PKGDATADIR=/usr/share/pbuilder DEB_HOST_ARCH_BITS=64 LANG=C MAKEFLAGS=w DEB_TARGET_ARCH=amd64 DH_INTERNAL_OPTIONS='-O--buildsystem=meson-O--builddir=build' DEB_HOST_GNU_CPU=x86_64 DEB_BUILD_ARCH_LIBC=gnu BUILDUSERNAME=pbuilder1 MFLAGS=-w DEB_TARGET_ARCH_BITS=64 CXXFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' ASFLAGS='' DEB_BUILD_ARCH_CPU=amd64 LD_PRELOAD='' DEB_HOST_ARCH_OS=linux SHELL=/bin/bash SHLVL=2 DEB_HOST_ARCH_CPU=amd64 FCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PBCURRENTCOMMANDLINEOPERATION=build DEB_BUILD_ARCH_ABI=base LANGUAGE=en_US:en PBUILDER_SYSCONFDIR=/etc CPPFLAGS_FOR_BUILD='-Wdate-time -D_FORTIFY_SOURCE=2' DEB_BUILD_ARCH=amd64 FFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' DEB_HOST_ARCH_LIBC=gnu TZ=/usr/share/zoneinfo/Etc/GMT+12 INVOCATION_ID=6b5af96ba47d42faa9b73692c01308e3 SUDO_GID=110 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.XqQj8OYE/pbuilderrc_FjDx --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XqQj8OYE/b1 --logfile b1/build.log freebayes_1.3.7-1~exp.dsc' DEB_TARGET_ARCH_CPU=amd64 DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_ARCH_OS=linux FCFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' DFLAGS_FOR_BUILD=-frelease LOGNAME=pbuilder1 CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' DEB_TARGET_MULTIARCH=x86_64-linux-gnu DEB_BUILD_GNU_CPU=x86_64 DEB_TARGET_ARCH_OS=linux USER=pbuilder1 DEB_HOST_ARCH_ABI=base DEB_BUILD_MULTIARCH=x86_64-linux-gnu LDFLAGS='-Wl,-z,relro -Wl,-z,now' DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_ABI=base _=/usr/bin/unshare CFLAGS='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' SUDO_USER=jenkins DFLAGS=-frelease PBUILDER_PKGLIBDIR=/usr/lib/pbuilder DEB_TARGET_GNU_CPU=x86_64 ASFLAGS_FOR_BUILD='' DEBIAN_FRONTEND=noninteractive HOME=/build/reproducible-path/freebayes-1.3.7/debian/.debhelper/generated/_source/home DEB_RULES_REQUIRES_ROOT=no DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_HOST_ARCH_ENDIAN=little TERM=unknown OBJCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' DEB_BUILD_MAINT_OPTIONS=hardening=+all DH_INTERNAL_BUILDFLAGS=1 CXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' DH_INTERNAL_OVERRIDE=dh_auto_test PBUILDER_OPERATION=build MAKELEVEL=2 XDG_RUNTIME_DIR=/tmp/dh-xdg-rundir-lzu88t_M MESON_TESTTHREADS=42 DEB_PYTHON_INSTALL_LAYOUT=deb ==================================== 5/5 ===================================== test: T03 start time: 20:40:16 duration: 2.42s result: exit status 1 command: MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=93 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/03_reference_bases.t ----------------------------------- stdout ----------------------------------- t/03_reference_bases.t .. 1..3 ok 1 - freebayes rejects invalid reference not ok 2 - freebayes does not put uppercase IUPAC bases in VCFs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 14 . A G # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA # ref 29 . C G # ref 31 . A T' not ok 3 - freebayes does not put lowercase IUPAC bases in VCFs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 14 . A G # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA # ref 29 . C G # ref 31 . A T' Failed 2/3 subtests Test Summary Report ------------------- t/03_reference_bases.t (Wstat: 0 Tests: 3 Failed: 2) Failed tests: 2-3 Files=1, Tests=3, 2 wallclock secs ( 0.04 usr 1.91 sys + 0.06 cusr 0.07 csys = 2.08 CPU) Result: FAIL ============================================================================== ==================================== 1/5 ===================================== test: T00 start time: 20:40:16 duration: 2.74s result: exit status 1 command: MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=42 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t ----------------------------------- stdout ----------------------------------- t/00_region_and_target_handling.t .. 1..12 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty not ok 3 - ref:5-6 ref:7-8 not ok 4 - ref:5 ref:7 not ok 5 - ref:5- not ok 6 - full output not ok 7 - --targets t/../00_region_and_target_handling.t.bed not ok 8 - --region ref not ok 9 - ref:1,0- not ok 10 - ref:1,0-1,1 not ok 11 - ref:0-1 ok 12 - region outside of bounds error Failed 9/12 subtests Test Summary Report ------------------- t/00_region_and_target_handling.t (Wstat: 0 Tests: 12 Failed: 9) Failed tests: 3-11 Files=1, Tests=12, 2 wallclock secs ( 0.04 usr 0.02 sys + 1.36 cusr 0.14 csys = 1.56 CPU) Result: FAIL ----------------------------------- stderr ----------------------------------- /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:5-6 ref:7-8' # at t/00_region_and_target_handling.t line 101. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:5 ref:7' # at t/00_region_and_target_handling.t line 104. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:5-' # at t/00_region_and_target_handling.t line 113. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'full output' # at t/00_region_and_target_handling.t line 124. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test '--targets t/../00_region_and_target_handling.t.bed' # at t/00_region_and_target_handling.t line 127. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test '--region ref' # at t/00_region_and_target_handling.t line 130. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:1,0-' # at t/00_region_and_target_handling.t line 138. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. # Failed test 'ref:1,0-1,1' # at t/00_region_and_target_handling.t line 141. # Failed test 'ref:0-1' # at t/00_region_and_target_handling.t line 145. Output: /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. ============================================================================== ==================================== 4/5 ===================================== test: T02 start time: 20:40:16 duration: 3.18s result: exit status 1 command: MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=177 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/02_multi_bam.t ----------------------------------- stdout ----------------------------------- t/02_multi_bam.t .. 1..7 not ok 1 - freebayes calls from two identical BAMs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' not ok 2 - freebayes calls from two BAMs with different samples for different read groups # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' not ok 3 - freebayes calls from two BAMs with different technologies for different read groups # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups not ok 6 - freebayes calls multiple alts from two different BAMs # got: '/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.' # expected: 'ref 2 . A C,G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' ok 7 - freebayes rejects two BAMs with the same name Failed 4/7 subtests Test Summary Report ------------------- t/02_multi_bam.t (Wstat: 0 Tests: 7 Failed: 4) Failed tests: 1-3, 6 Files=1, Tests=7, 3 wallclock secs ( 1.93 usr 0.01 sys + 0.20 cusr 0.25 csys = 2.39 CPU) Result: FAIL ============================================================================== ==================================== 2/5 ===================================== test: T01 start time: 20:40:16 duration: 3.85s result: exit status 1 command: MALLOC_PERTURB_=137 MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01_call_variants.t ----------------------------------- stdout ----------------------------------- t/01_call_variants.t .. 1..16 not ok 1 - variant calling recovers most of the GiAB variants in a test region # got: '0' # expected: '1' ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference not ok 5 - freebayes processes all alignments in BAM input # got: '3333' # expected: '51' ok 6 - freebayes processes all alignments in CRAM input not ok 7 - freebayes correctly handles variant input # got: '0' # expected: '16' not ok 8 - freebayes puts required variants in output # got: '0' # expected: '3' not ok 9 - freebayes limits calls to input variants correctly # got: '0' # expected: '3' not ok 10 - freebayes reports all input variants even when there is no input data # got: '0' # expected: '16' not ok 11 - freebayes handles region and variant input # got: '0' # expected: '2' not ok 12 - freebayes limits to variant input correctly when region is given # got: '0' # expected: '2' not ok 13 - freebayes handles variant input and reading from stdin # got: '0' # expected: '3' not ok 14 - freebayes limits to variant input when reading from stdin # got: '0' # expected: '3' not ok 15 - freebayes handles region, stdin, and variant input # got: '0' # expected: '2' ok 16 - ! Failed 11/16 subtests Test Summary Report ------------------- t/01_call_variants.t (Wstat: 0 Tests: 16 Failed: 11) Failed tests: 1, 5, 7-15 Files=1, Tests=16, 4 wallclock secs ( 0.06 usr 0.02 sys + 0.73 cusr 2.31 csys = 3.12 CPU) Result: FAIL ----------------------------------- stderr ----------------------------------- /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. t/01_call_variants.t: line 107: 2781630 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null ============================================================================== ==================================== 3/5 ===================================== test: T01b start time: 20:40:16 duration: 4.44s result: exit status 1 command: MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=198 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01b_call_variants.t ----------------------------------- stdout ----------------------------------- t/01b_call_variants.t .. 1..10 ok 1 - running in parallel makes no difference ok 2 - freebayes handles spaces in file names not ok 3 - freebayes handles region and variant input even with : in contig names # got: '0' # expected: '2' not ok 4 - freebayes can handle spliced reads # got: '0' # expected: '3' not ok 5 - freebayes produces the expected number of lines of gVCF output # got: '0' # expected: '20' not ok 6 - freebayes produces the expected number of lines of gVCF output # got: '3' # expected: '250' not ok 7 - freebayes produces the expected number of lines of gVCF output # got: '176' # expected: '12250' not ok 8 - the CNV map may be used to specify per-sample copy numbers # got: '0' # expected: '19' not ok 9 - freebayes makes the expected number of calls when capping coverage # got: '0' # expected: '22' not ok 10 - freebayes correctly uses CNV map with multiple entries # got: '0:0' # expected: '0:19' Failed 8/10 subtests Test Summary Report ------------------- t/01b_call_variants.t (Wstat: 0 Tests: 10 Failed: 8) Failed tests: 3-10 Files=1, Tests=10, 2 wallclock secs ( 0.05 usr 0.01 sys + 1.06 cusr 0.54 csys = 1.66 CPU) Result: FAIL ----------------------------------- stderr ----------------------------------- /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. /usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. ============================================================================== Summary of Failures: 5/5 T03 FAIL 2.42s exit status 1 1/5 T00 FAIL 2.74s exit status 1 4/5 T02 FAIL 3.18s exit status 1 2/5 T01 FAIL 3.85s exit status 1 3/5 T01b FAIL 4.44s exit status 1 Ok: 0 Expected Fail: 0 Fail: 5 Unexpected Pass: 0 Skipped: 0 Timeout: 0 dh_auto_test: error: cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=42 meson test -v --timeout-multiplier 100 returned exit code 5 make[1]: *** [debian/rules:14: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/freebayes-1.3.7' make: *** [debian/rules:6: 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/2765857 and its subdirectories