Tue May 14 20:21:46 UTC 2024 I: starting to build freebayes/experimental/arm64 on jenkins on '2024-05-14 20:21' Tue May 14 20:21:46 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_19/18319/console.log Tue May 14 20:21:46 UTC 2024 I: Downloading source for experimental/freebayes=1.3.7-1~exp --2024-05-14 20:21:46-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/freebayes/freebayes_1.3.7-1%7eexp.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2248 (2.2K) [text/prs.lines.tag] Saving to: ‘freebayes_1.3.7-1~exp.dsc’ 0K .. 100% 329M=0s 2024-05-14 20:21:46 (329 MB/s) - ‘freebayes_1.3.7-1~exp.dsc’ saved [2248/2248] Tue May 14 20:21:46 UTC 2024 I: freebayes_1.3.7-1~exp.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: freebayes Binary: freebayes Architecture: any Version: 1.3.7-1~exp Maintainer: Debian Med Packaging Team Uploaders: Brad Chapman , Andreas Tille Homepage: https://github.com/ekg/freebayes Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/freebayes Vcs-Git: https://salsa.debian.org/med-team/freebayes.git Testsuite: autopkgtest Build-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 Package-List: freebayes deb science optional arch=any Checksums-Sha1: aa5e76b874f5daa90102152d542fa30f5bac701f 2901909 freebayes_1.3.7.orig.tar.gz 8aaefbb3a7c49bb427a55d0d7467de8375902b4f 11520 freebayes_1.3.7-1~exp.debian.tar.xz Checksums-Sha256: 73de20987bfad317099e5bb2f651073351906b9fb1392d704332f401fbfbb5c6 2901909 freebayes_1.3.7.orig.tar.gz 0f519dcc9bf9719da911c72de41ab570fd90b7beb38055300fe40707e0d7fc6b 11520 freebayes_1.3.7-1~exp.debian.tar.xz Files: 83a9eaef72b98e3c03c287ec73c69687 2901909 freebayes_1.3.7.orig.tar.gz 23ee4258177f9ae2036b3c3933b3a55e 11520 freebayes_1.3.7-1~exp.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmQJs5MRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFiqA//Yp+HF/XQCHmX6Hm8esMsdJtxdxs3QVH3 xqzdn9obKJIhXQa2i6nYjwnZsNZndSocGHMPJWjc9kmNlmc8wNjOyTUXyafkOaRC AUgeixXYmLslBSZPdhVmGDcMrDRucup1N6xMrWMoi5IB6xyzVEmQudHP6XVteEQI 6EoqpF8M4gzpMBnMnRqLXTxsMBAqPxq9j/VvI3xMxe4BpkSXK19BY7h43RRbeSpd TSku4BKih72JHZMfipg21tRxVA3YwxL8Eempe3R0Gu2riWNz1hgETim2BQaSQf55 313bdaclHgZBOSWSiPYcQpZs3sXE1lrgLeX7dlGSPRAXYO7JKI0w05Z1vVuoyeAO mPCpQVyZzdagDlQtIGYHEo7ZB5IShgs7H06xNjcb+W2s3m+dLa4G61YpDlTTNyfR x8x7sw56LF60YfP6vQp0GG41UwxchNBPbkaGBsuqv0pBIH2FcM2AJbv5/Jk/6f/c sHVrUd+9E4uqRKzoDNyOyQD/Vyl5hKQkyJuQe9jtHoAEnVlg7d1NYdEZx2sd/3LY clLH9xfpWHL3/GShVDi5RiQgwN3zvjBIl6F4CQZK9DzqJ3pEhrxINQ9tGIUKXw4R ctlG8BMeEicv1osYPHBIqjM1Hd1cZwfAQrou+YIVWbdjVmEnVq44HoZsftIkKbfY CLUzJtN1zec= =kuHY -----END PGP SIGNATURE----- Tue May 14 20:21:46 UTC 2024 I: Checking whether the package is not for us Tue May 14 20:21:46 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Tue May 14 20:21:46 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Tue May 14 20:23:03 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 14 08:21:49 -12 2024 I: pbuilder-time-stamp: 1715718109 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/2106325/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='baacbc94a7914fc9823691d1b3ca2128' 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='2106325' 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.wZSSnV9r/pbuilderrc_SyGK --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.wZSSnV9r/b1 --logfile b1/build.log freebayes_1.3.7-1~exp.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 07:34 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2106325/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19745 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} 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} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas3{a} libbrotli1{a} libbsd0{a} libbwa-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} 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} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp-dev{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{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} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{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} libssh2-1t64{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{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} littler{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} ninja-build{a} openssl{a} parallel{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} r-base{a} r-base-core{a} r-cran-boot{a} r-cran-class{a} r-cran-cli{a} r-cran-cluster{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-foreign{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-kernsmooth{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-nnet{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-rpart{a} r-cran-scales{a} r-cran-spatial{a} r-cran-survival{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} r-recommended{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 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 libx11-protocol-perl lynx psmisc publicsuffix r-base-dev r-base-html 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-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-pkgdown r-cran-processx r-cran-profvis r-cran-ps r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-vdiffr r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 213 newly installed, 0 to remove and 0 not upgraded. Need to get 126 MB of archives. After unpacking 323 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.1-1 [93.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 bc arm64 1.07.1-4 [101 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 42 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-5 [141 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libbamtools-dev arm64 2.5.2+dfsg-5 [212 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbwa-dev arm64 0.7.17-7+b3 [147 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-1 [114 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-1 [105 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 79 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.7.1-5 [405 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.7.1-5 [524 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.7.1-5 [412 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b1 [4880 B] Get: 95 http://deb.debian.org/debian unstable/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4+b1 [4856 B] Get: 96 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b1 [24.6 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b1 [27.0 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14-20240429-1 [361 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.80.2-1 [1393 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libjsoncpp-dev arm64 1.9.5-6+b2 [24.8 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.52.2+ds-1 [206 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.52.2+ds-1 [45.5 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.52.2+ds-1 [33.0 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 125 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libssw0 arm64 1.1-14+b1 [19.6 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libseqlib2 arm64 1.2.0+dfsg-11+b1 [144 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libssw-dev arm64 1.1-14+b1 [117 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libseqlib-dev arm64 1.2.0+dfsg-11+b1 [208 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b1 [32.7 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b1 [38.4 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libtabixpp0t64 arm64 1.1.2-2.1 [9296 B] Get: 137 http://deb.debian.org/debian unstable/main arm64 libtabixpp-dev arm64 1.1.2-2.1 [9004 B] Get: 138 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1 [975 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.14-1 [732 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libwfa2-0 arm64 2.3.3-4 [55.0 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libvcflib2 arm64 1.0.9+dfsg1-3+b1 [161 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libwfa2-dev arm64 2.3.3-4 [74.7 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libvcflib-dev arm64 1.0.9+dfsg1-3+b1 [77.8 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-13 [223 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.0-2 [27.9 MB] Get: 155 http://deb.debian.org/debian unstable/main arm64 r-cran-littler arm64 0.3.20-1 [102 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 littler all 0.3.20-1 [16.0 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 r-cran-rcpp arm64 1.0.12-1 [2054 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 r-cran-plyr arm64 1.8.9-1 [829 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 r-cran-cli arm64 3.6.2-1 [1320 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 r-cran-glue arm64 1.7.0-1 [156 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 r-cran-isoband arm64 0.2.7-1 [1612 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 r-cran-mass arm64 7.3-60.2-1 [1111 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 r-cran-lattice arm64 0.22-6-1 [1391 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 r-cran-nlme arm64 3.1.164-1 [2276 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 r-cran-boot all 1.3-30-1 [622 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 r-cran-cluster arm64 2.1.6-1 [563 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 r-cran-foreign arm64 0.8.86-1 [245 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 r-cran-kernsmooth arm64 2.23-22-1 [90.1 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 r-cran-survival arm64 3.6-4-1 [6289 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 r-cran-rpart arm64 4.1.23-1 [682 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 r-cran-class arm64 7.3-22-2 [87.2 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 r-cran-spatial arm64 7.3-17-1 [128 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 r-recommended all 4.4.0-2 [2572 B] Get: 180 http://deb.debian.org/debian unstable/main arm64 r-base all 4.4.0-2 [14.3 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 r-cran-matrix arm64 1.7-0-2 [4003 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 r-cran-mgcv arm64 1.9-1-1 [3206 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 r-cran-farver arm64 2.1.1-2 [1390 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1690 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 r-cran-scales all 1.3.0-1 [677 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 r-cran-magrittr arm64 2.0.3-1 [200 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 r-cran-utf8 arm64 1.2.4-1 [132 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 r-cran-vctrs arm64 0.6.5-1 [1354 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [420 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libvcflib-tools arm64 1.0.9+dfsg1-3+b1 [578 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 ninja-build arm64 1.12.1-1 [128 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 meson all 1.4.0-2 [603 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 sysstat arm64 12.7.5-2 [596 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 parallel all 20240222+ds-2 [2163 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.19.2-1+b1 [617 kB] Fetched 126 MB in 1s (154 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19745 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20061 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... 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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 arm64 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/aarch64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.4.0 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 13.2.0 "cc (Debian 13.2.0-24) 13.2.0") C linker for the host machine: cc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Debian 13.2.0-24) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 Host machine cpu family: aarch64 Host machine cpu: aarch64 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 5.4.5 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.19 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/aarch64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 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 -j12 -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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 [10/27] 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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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); | ~~~~^~~~~ [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ../src/Marginals.h:4: /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../src/DataLikelihood.h:4: /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 [19/27] 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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 In file included from ../contrib/ttmath/ttmathint.h:48, from ../contrib/ttmath/ttmathbig.h:46, from ../contrib/ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Exp(const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../contrib/ttmath/ttmath.h:326:10, inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘x.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘BigFloat big_exp(long double)’: ../src/Utility.cpp:361:14: note: ‘x’ declared here 361 | BigFloat x, result; | ^ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Exp(const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../contrib/ttmath/ttmath.h:326:10, inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘x.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘BigFloat big_exp(long double)’: ../src/Utility.cpp:361:14: note: ‘x’ declared here 361 | BigFloat x, result; | ^ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big ttmath::Big::operator+(const ttmath::Big&) const [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:5570:15, inlined from ‘long double logsumexp_probs(const std::vector&)’ at ../src/Utility.cpp:381:48: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘maxNb.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘long double logsumexp_probs(const std::vector&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big ttmath::Big::operator+(const ttmath::Big&) const [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:5570:15, inlined from ‘long double logsumexp_probs(const std::vector&)’ at ../src/Utility.cpp:381:48: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘maxNb.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘long double logsumexp_probs(const std::vector&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ [21/27] 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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ../src/ResultData.h:4: /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [23/27] 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 -mbranch-protection=standard -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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../src/freebayes.cpp:9: /usr/include/c++/13/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++/13/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 -mbranch-protection=standard -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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../src/AlleleParser.h:4: /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libtabixpp.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-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=12 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 >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=244 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t 2/5 T01 RUNNING >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=108 /usr/bin/prove -e bash -v t/01_call_variants.t 3/5 T01b RUNNING >>> MALLOC_PERTURB_=27 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_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 >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=12 UBSAN_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 >>> MALLOC_PERTURB_=211 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_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 0.18s 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.02 cusr 0.02 csys = 0.07 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 1/5 T00 FAIL 0.32s 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, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.09 cusr 0.07 csys = 0.18 CPU) Result: FAIL stderr: /usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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 0.35s exit status 1 ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/02_multi_bam.t .. 1..7 not ok 1 - freebayes calls from two identical BAMs # got: '/usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.11 cusr 0.06 csys = 0.20 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 2/5 T01 FAIL 0.62s 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, 0 wallclock secs ( 0.03 usr 0.00 sys + 0.34 cusr 0.16 csys = 0.53 CPU) Result: FAIL stderr: /usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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: 2145673 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 0.64s 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, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.38 cusr 0.27 csys = 0.67 CPU) Result: FAIL stderr: /usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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 0.18s exit status 1 1/5 T00 FAIL 0.32s exit status 1 4/5 T02 FAIL 0.35s exit status 1 2/5 T01 FAIL 0.62s exit status 1 3/5 T01b FAIL 0.64s 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 2024-05-14T08:23:01.281485 Inherited environment: DEB_HOST_MULTIARCH=aarch64-linux-gnu LC_ALL=C.UTF-8 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=aarch64-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 -mbranch-protection=standard' SUDO_UID=104 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_GNU_SYSTEM=linux-gnu CFLAGS_FOR_BUILD='-g -O2' OBJCXXFLAGS_FOR_BUILD='-g -O2' DEB_BUILD_ARCH_BITS=64 DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DEB_HOST_ARCH=arm64 LDFLAGS_FOR_BUILD='' 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' OBJCXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard' OLDPWD=/ PBUILDER_PKGDATADIR=/usr/share/pbuilder DEB_HOST_ARCH_BITS=64 LANG=C MAKEFLAGS=w DEB_TARGET_ARCH=arm64 DH_INTERNAL_OPTIONS='-O--buildsystem=meson-O--builddir=build' DEB_HOST_GNU_CPU=aarch64 DEB_BUILD_ARCH_LIBC=gnu BUILDUSERNAME=pbuilder1 MFLAGS=-w DEB_TARGET_ARCH_BITS=64 CXXFLAGS_FOR_BUILD='-g -O2' ASFLAGS='' DEB_BUILD_ARCH_CPU=arm64 LD_PRELOAD='' DEB_HOST_ARCH_OS=linux SHELL=/bin/bash SHLVL=2 DEB_HOST_ARCH_CPU=arm64 FCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.7=. -fstack-protector-strong -fstack-clash-protection -mbranch-protection=standard' 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='' DEB_BUILD_ARCH=arm64 FFLAGS_FOR_BUILD='-g -O2' DEB_HOST_ARCH_LIBC=gnu TZ=/usr/share/zoneinfo/Etc/GMT+12 INVOCATION_ID=549b0e922d5f43d19b54ae7054cf5f87 SUDO_GID=109 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.wZSSnV9r/pbuilderrc_SyGK --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.wZSSnV9r/b1 --logfile b1/build.log freebayes_1.3.7-1~exp.dsc' DEB_TARGET_ARCH_CPU=arm64 DEB_HOST_GNU_TYPE=aarch64-linux-gnu DEB_BUILD_ARCH_OS=linux FCFLAGS_FOR_BUILD='-g -O2' 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=aarch64-linux-gnu DEB_BUILD_GNU_CPU=aarch64 DEB_TARGET_ARCH_OS=linux USER=pbuilder1 DEB_HOST_ARCH_ABI=base DEB_BUILD_MULTIARCH=aarch64-linux-gnu LDFLAGS='-Wl,-z,relro -Wl,-z,now' DEB_TARGET_GNU_TYPE=aarch64-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 -mbranch-protection=standard' SUDO_USER=jenkins DFLAGS=-frelease PBUILDER_PKGLIBDIR=/usr/lib/pbuilder DEB_TARGET_GNU_CPU=aarch64 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 -mbranch-protection=standard' 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 -mbranch-protection=standard' DH_INTERNAL_OVERRIDE=dh_auto_test PBUILDER_OPERATION=build MAKELEVEL=2 XDG_RUNTIME_DIR=/tmp/dh-xdg-rundir-UIp6iHWj DEB_PYTHON_INSTALL_LAYOUT=deb MESON_TESTTHREADS=12 ==================================== 5/5 ===================================== test: T03 start time: 20:23:01 duration: 0.18s result: exit status 1 command: MALLOC_PERTURB_=211 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.02 cusr 0.02 csys = 0.07 CPU) Result: FAIL ============================================================================== ==================================== 1/5 ===================================== test: T00 start time: 20:23:01 duration: 0.32s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=244 /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, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.09 cusr 0.07 csys = 0.18 CPU) Result: FAIL ----------------------------------- stderr ----------------------------------- /usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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: 20:23:01 duration: 0.35s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=12 UBSAN_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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.11 cusr 0.06 csys = 0.20 CPU) Result: FAIL ============================================================================== ==================================== 2/5 ===================================== test: T01 start time: 20:23:01 duration: 0.62s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=108 /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, 0 wallclock secs ( 0.03 usr 0.00 sys + 0.34 cusr 0.16 csys = 0.53 CPU) Result: FAIL ----------------------------------- stderr ----------------------------------- /usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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: 2145673 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: 20:23:01 duration: 0.64s result: exit status 1 command: MALLOC_PERTURB_=27 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_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, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.38 cusr 0.27 csys = 0.67 CPU) Result: FAIL ----------------------------------- stderr ----------------------------------- /usr/include/c++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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++/13/bits/stl_vector.h:1128: 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 0.18s exit status 1 1/5 T00 FAIL 0.32s exit status 1 4/5 T02 FAIL 0.35s exit status 1 2/5 T01 FAIL 0.62s exit status 1 3/5 T01b FAIL 0.64s 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=12 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/2106325 and its subdirectories Tue May 14 20:23:04 UTC 2024 W: No second build log, what happened?