Tue Apr 18 04:48:56 UTC 2023 I: starting to build freebayes/bookworm/arm64 on jenkins on '2023-04-18 04:48' Tue Apr 18 04:48:56 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/25883/console.log Tue Apr 18 04:48:56 UTC 2023 I: Downloading source for bookworm/freebayes=1.3.6-2 --2023-04-18 04:48:56-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/freebayes/freebayes_1.3.6-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2232 (2.2K) [text/prs.lines.tag] Saving to: ‘freebayes_1.3.6-2.dsc’ 0K .. 100% 1.63M=0.001s 2023-04-18 04:48:56 (1.63 MB/s) - ‘freebayes_1.3.6-2.dsc’ saved [2232/2232] Tue Apr 18 04:48:56 UTC 2023 I: freebayes_1.3.6-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: freebayes Binary: freebayes Architecture: any Version: 1.3.6-2 Maintainer: Debian Med Packaging Team Uploaders: Brad Chapman , Andreas Tille Homepage: https://github.com/ekg/freebayes Standards-Version: 4.6.1 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: 2513323e336e02b5cc83d43c9f5b725579c0b75a 2898209 freebayes_1.3.6.orig.tar.gz 504b332ace3ff066468126e5559e058877bdfa0c 11440 freebayes_1.3.6-2.debian.tar.xz Checksums-Sha256: d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044 2898209 freebayes_1.3.6.orig.tar.gz 2fbada9aaa038dc048d99a28e91201f4b57f240a5119fd01e83bdf3224e63872 11440 freebayes_1.3.6-2.debian.tar.xz Files: e8fe2bf8bb0139bb313744e5fb8e4105 2898209 freebayes_1.3.6.orig.tar.gz cd9f68ade2865de3a9d15cab4fce73fe 11440 freebayes_1.3.6-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNhIusRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtExzQ/7ByePtBFO7BmSz+2yth7yzj4R9ki7MfIB gqDj+ED4wmsVi2dsdA+21ap7+lbWYvJ43m41fMqPGneDpQql0LVrqQhvimfMHR9k ZkpdlmptasFcYuitAQwWq1tCuOBprjKkcUK91sfu/U9Sax9v1QkLb2iG1eW4hWEG j6aZRTY2EDB0Dmu9YXQ7MgwCQ2DO7qDLK9dDh6HkbpSgXH8vnnamU8uUg0FhgcWI L/wx/s0tiOcKEpJQTwCEc38lSgRRmEDREkyGebRy+qwXZS5Ny768UtrTr0tD9E7P EkXVm6toysJkzHeHxQV2ZE7IvThQGrwSqnD1uIp54PbVNw6VOR7wy0etAw7Z4nGB UL5kG+F93NH3OvUjJtt+3W9Uow/GKydF5t/qyTPDJmhyKX5eHFnLNv7HHFPKFIaJ D6S+0GOjZPZ+qB/WmUKxlorZiL+L9DwHitqL9IV5smJjUP5n7nbCe/bMzYJNtDHP vR3TWMGTv38iBieROZ6bYRe2N9VUVZPlFtG+DJledJVlUieGqhuZSh0aoP9j6sr5 NKFqvBkEUuiLXVHyqNMOQ8uf6qxbwl/pKFBfeWaawCC5jIbjFrxudmRpfPv8oC+3 iJbcuuAa04hsIsNRj4h9gmJFlklcEDlYIilcoKaD0WBdmTAbB+Ak3WxN26fN894G VVCnkpOIsXI= =jOZ7 -----END PGP SIGNATURE----- Tue Apr 18 04:48:56 UTC 2023 I: Checking whether the package is not for us Tue Apr 18 04:48:56 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Tue Apr 18 04:48:56 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Tue Apr 18 04:52:20 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 19 23:12:00 -12 2024 I: pbuilder-time-stamp: 1716203520 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.3.6-2.dsc] I: copying [./freebayes_1.3.6.orig.tar.gz] I: copying [./freebayes_1.3.6-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 1 01:45:15 2022 -12 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_1.3.6-2.dsc: no acceptable signature found dpkg-source: info: extracting freebayes in freebayes-1.3.6 dpkg-source: info: unpacking freebayes_1.3.6.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.6-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29651/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='29651' 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.e95NGE8P/pbuilderrc_7DQ9 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.e95NGE8P/b1 --logfile b1/build.log freebayes_1.3.6-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 19 04:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29651/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 ... 19616 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} 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} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1{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} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp-dev{a} libjsoncpp25{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{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} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib-dev{a} libseqlib2{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib1{a} libwebp7{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} libxt6{a} littler{a} m4{a} man-db{a} media-types{a} meson{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-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samtools{a} sensible-utils{a} sysstat{a} 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 curl 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-cran-abind r-cran-bit64 r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-domc r-cran-dplyr r-cran-formattable r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-interp r-cran-knitr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rsqlite r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-vdiffr r-cran-waldo r-cran-xml2 r-doc-html r-recommended shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 187 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After unpacking 292 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 bc arm64 1.07.1-3 [107 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 fontconfig arm64 2.14.1-4 [449 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libbamtools-dev arm64 2.5.2+dfsg-4 [204 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libbwa-dev arm64 0.7.17-7+b2 [147 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libpixman-1-0 arm64 0.42.2-1 [470 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libcairo2 arm64 1.16.0-7 [527 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-8 [357 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-8 [466 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libdatrie1 arm64 0.2.13-2+b1 [42.6 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b1 [4880 B] Get: 86 http://deb.debian.org/debian bookworm/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4+b1 [4856 B] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libfastahack0 arm64 1.0.0+dfsg-10 [23.8 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 libfastahack-dev arm64 1.0.0+dfsg-10 [26.1 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp-dev arm64 1.9.5-4 [26.4 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libthai-data all 0.1.29-1 [176 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libthai0 arm64 0.1.29-1 [56.2 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libpango-1.0-0 arm64 1.50.12+ds-1 [200 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libpangoft2-1.0-0 arm64 1.50.12+ds-1 [44.5 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libpangocairo-1.0-0 arm64 1.50.12+ds-1 [32.0 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libpaper1 arm64 1.1.29 [12.6 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libpaper-utils arm64 1.1.29 [8776 B] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libsensors5 arm64 1:3.6.0-7.1 [33.3 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libssw0 arm64 1.1-13 [18.5 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libseqlib2 arm64 1.2.0+dfsg-9 [141 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libssw-dev arm64 1.1-13 [21.9 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libseqlib-dev arm64 1.2.0+dfsg-9 [202 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b1 [32.7 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b1 [38.4 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libtabixpp0 arm64 1.1.2-1 [9120 B] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libtabixpp-dev arm64 1.1.2-1 [8756 B] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [973 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 libxft2 arm64 2.3.6-1 [58.7 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libtk8.6 arm64 8.6.13-2 [729 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libvcflib1 arm64 1.0.3+dfsg-2 [132 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libvcflib-dev arm64 1.0.3+dfsg-2 [85.2 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 zip arm64 3.0-13 [223 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 unzip arm64 6.0-28 [157 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libxt6 arm64 1:1.2.1-1.1 [172 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 r-base-core arm64 4.2.2.20221110-2 [25.7 MB] Get: 141 http://deb.debian.org/debian bookworm/main arm64 r-cran-littler arm64 0.3.17-1 [95.6 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 littler all 0.3.17-1 [14.4 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 r-cran-rcpp arm64 1.0.10-1 [2043 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 r-cran-plyr arm64 1.8.8-1 [830 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 r-cran-cli arm64 3.6.0-1 [1282 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 r-cran-glue arm64 1.6.2-1 [152 kB] Get: 148 http://deb.debian.org/debian bookworm/main arm64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get: 149 http://deb.debian.org/debian bookworm/main arm64 r-cran-isoband arm64 0.2.7-1 [1612 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 r-cran-rlang arm64 1.0.6-1 [1614 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 r-cran-mass arm64 7.3-58.2-1 [1120 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 r-cran-lattice arm64 0.20-45-3 [1175 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 r-cran-nlme arm64 3.1.162-1 [2255 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 r-cran-matrix arm64 1.5-3-1 [3757 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 r-cran-mgcv arm64 1.8-41-1 [3144 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 r-cran-farver arm64 2.1.1-1 [1388 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1690 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 r-cran-scales all 1.2.1-1 [614 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 r-cran-fansi arm64 1.0.4-1 [615 kB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 r-cran-magrittr arm64 2.0.3-1 [200 kB] Get: 167 http://deb.debian.org/debian bookworm/main arm64 r-cran-utf8 arm64 1.2.3-1 [132 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 r-cran-vctrs arm64 0.5.2-1 [1350 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 r-cran-tibble arm64 3.1.8+dfsg-1 [513 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 r-cran-withr all 2.5.0-1 [236 kB] Get: 173 http://deb.debian.org/debian bookworm/main arm64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 175 http://deb.debian.org/debian bookworm/main arm64 libvcflib-tools arm64 1.0.3+dfsg-2 [667 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 ninja-build arm64 1.11.1-1 [127 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 meson all 1.0.1-5 [548 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 sysstat arm64 12.6.1-1 [570 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 parallel all 20221122+ds-2 [1873 kB] Get: 184 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] Fetched 111 MB in 6s (19.4 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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20366 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../007-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... 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Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20221122+ds-2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../173-pkgconf-bin_1.8.1-1_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../174-pkgconf_1.8.1-1_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../175-pkg-config_1.8.1-1_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-1) ... Selecting previously unselected package samtools. Preparing to unpack .../176-samtools_1.16.1-1_arm64.deb ... Unpacking samtools (1.16.1-1) ... Setting up libhtscodecs2:arm64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... 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Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libfml-dev:arm64 (0.1+git20190320.b499514-1+b1) ... Setting up libssw-dev:arm64 (1.1-13) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up bc (1.07.1-3) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up pkgconf:arm64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ... Setting up libbamtools-dev:arm64 (2.5.2+dfsg-4) ... Setting up pkg-config:arm64 (1.8.1-1) ... Setting up libsmithwaterman-dev:arm64 (0.0+git20160702.2610e25-12+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:arm64 (7.88.1-8) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up sysstat (12.6.1-1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libpaper1:arm64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libpango-1.0-0:arm64 (1.50.12+ds-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:arm64 (7.88.1-8) ... Setting up libpaper-utils (1.1.29) ... Setting up libcurl4-gnutls-dev:arm64 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.16.0-7) ... Setting up libxt6:arm64 (1:1.2.1-1.1) ... Setting up parallel (20221122+ds-2) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:arm64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:arm64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libhts3:arm64 (1.16+ds-3) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up libhts-dev:arm64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up samtools (1.16.1-1) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-nlme (3.1.162-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up libtabixpp0:arm64 (1.1.2-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libseqlib2:arm64 (1.2.0+dfsg-9) ... Setting up r-cran-littler (0.3.17-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up r-cran-rcpp (1.0.10-1) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.17-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up libseqlib-dev:arm64 (1.2.0+dfsg-9) ... Setting up meson (1.0.1-5) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-plyr (1.8.8-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up libvcflib1:arm64 (1.0.3+dfsg-2) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up libtabixpp-dev:arm64 (1.1.2-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up libvcflib-dev:arm64 (1.0.3+dfsg-2) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up r-cran-scales (1.2.1-1) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up libvcflib-tools (1.0.3+dfsg-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/freebayes-1.3.6/ && 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_1.3.6-2_source.changes dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.6-2 dpkg-buildpackage: info: source distribution unstable 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 && LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu The Meson build system Version: 1.0.1 Source dir: /build/freebayes-1.3.6 Build dir: /build/freebayes-1.3.6/build Build type: native build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: cc (gcc 12.2.0 "cc (Debian 12.2.0-14) 12.2.0") C linker for the host machine: cc ld.bfd 2.40 C++ compiler for the host machine: c++ (gcc 12.2.0 "c++ (Debian 12.2.0-14) 12.2.0") C++ linker for the host machine: c++ ld.bfd 2.40 Host machine cpu family: aarch64 Host machine cpu: aarch64 Found pkg-config: /usr/bin/pkg-config (1.8.1) Run-time dependency zlib found: YES 1.2.13 Run-time dependency liblzma found: YES 5.4.1 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.16 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 Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j8 -v [1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 ‘seq’ 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 ‘seq’ 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); | ~~~~^~~~~ [9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from ../src/DataLikelihood.h:4: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from ../src/Marginals.h:4: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] 160 | switch (this->type) { | ^ ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] [16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 [19/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../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 ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Exp(const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:326:10, inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25: ../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 ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Exp(const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:326:10, inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25: ../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 ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../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 ../ttmath/ttmathbig.h:5570:15, inlined from ‘long double logsumexp_probs(const std::vector&)’ at ../src/Utility.cpp:381:48: ../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 ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../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]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../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 ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../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]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ [21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from ../src/ResultData.h:4: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from ../src/freebayes.cpp:9: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/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../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_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from ../src/AlleleParser.h:4: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/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/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/12/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/gcc/aarch64-linux-gnu/12/../../../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/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/12/../../../aarch64-linux-gnu/libtabixpp.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/12/../../../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/freebayes-1.3.6' mkdir -p test/bash-tap/ ln -s -t test/bash-tap /build/freebayes-1.3.6/debian/bash-tap/* mkdir -p test/test-simple-bash ln -s -t test/test-simple-bash /build/freebayes-1.3.6/debian/test-simple-bash/* dh_auto_test -- -v --timeout-multiplier 100 cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 ninja: no work to do. ninja: Entering directory `/build/freebayes-1.3.6/build' ninja: no work to do. 1/5 T00 RUNNING >>> MALLOC_PERTURB_=82 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t 2/5 T01 RUNNING >>> MALLOC_PERTURB_=103 /usr/bin/prove -e bash -v t/01_call_variants.t 3/5 T01b RUNNING >>> MALLOC_PERTURB_=121 /usr/bin/prove -e bash -v t/01b_call_variants.t 4/5 T02 RUNNING >>> MALLOC_PERTURB_=195 /usr/bin/prove -e bash -v t/02_multi_bam.t 5/5 T03 RUNNING >>> MALLOC_PERTURB_=97 /usr/bin/prove -e bash -v t/03_reference_bases.t 5/5 T03 OK 0.38s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/03_reference_bases.t .. 1..3 ok 1 - freebayes rejects invalid reference ok 2 - freebayes does not put uppercase IUPAC bases in VCFs ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. Files=1, Tests=3, 0 wallclock secs ( 0.07 usr 0.00 sys + 0.07 cusr 0.04 csys = 0.18 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 1/5 T00 OK 0.58s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― 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 ok 3 - ref:5-6 ref:7-8 ok 4 - ref:5 ref:7 ok 5 - ref:5- ok 6 - full output ok 7 - --targets t/../00_region_and_target_handling.t.bed ok 8 - --region ref ok 9 - ref:1,0- ok 10 - ref:1,0-1,1 ok 11 - ref:0-1 ok 12 - region outside of bounds error ok All tests successful. Files=1, Tests=12, 0 wallclock secs ( 0.06 usr 0.01 sys + 0.18 cusr 0.15 csys = 0.40 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 4/5 T02 OK 0.59s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/02_multi_bam.t .. 1..7 ok 1 - freebayes calls from two identical BAMs ok 2 - freebayes calls from two BAMs with different samples for different read groups ok 3 - freebayes calls from two BAMs with different technologies for different read groups 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 ok 6 - freebayes calls multiple alts from two different BAMs ok 7 - freebayes rejects two BAMs with the same name ok All tests successful. Files=1, Tests=7, 0 wallclock secs ( 0.07 usr 0.00 sys + 0.17 cusr 0.17 csys = 0.41 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 3/5 T01b OK 13.26s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/01b_call_variants.t .. 1..10 ok 1 - running in parallel makes no difference ok 2 - freebayes handles spaces in file names ok 3 - freebayes handles region and variant input even with : in contig names ok 4 - freebayes can handle spliced reads ok 5 - freebayes produces the expected number of lines of gVCF output ok 6 - freebayes produces the expected number of lines of gVCF output ok 7 - freebayes produces the expected number of lines of gVCF output ok 8 - the CNV map may be used to specify per-sample copy numbers ok 9 - freebayes makes the expected number of calls when capping coverage ok 10 - freebayes correctly uses CNV map with multiple entries ok All tests successful. Files=1, Tests=10, 13 wallclock secs ( 0.07 usr 0.01 sys + 13.54 cusr 0.62 csys = 14.24 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 2/5 T01 OK 26.44s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/01_call_variants.t .. 1..16 ok 1 - variant calling recovers most of the GiAB variants in a test region 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 ok 5 - freebayes processes all alignments in BAM input ok 6 - freebayes processes all alignments in CRAM input ok 7 - freebayes correctly handles variant input ok 8 - freebayes puts required variants in output ok 9 - freebayes limits calls to input variants correctly ok 10 - freebayes reports all input variants even when there is no input data ok 11 - freebayes handles region and variant input ok 12 - freebayes limits to variant input correctly when region is given ok 13 - freebayes handles variant input and reading from stdin ok 14 - freebayes limits to variant input when reading from stdin ok 15 - freebayes handles region, stdin, and variant input ok 16 - ! ok All tests successful. Files=1, Tests=16, 26 wallclock secs ( 0.07 usr 0.01 sys + 20.24 cusr 6.39 csys = 26.71 CPU) Result: PASS stderr: [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 t/01_call_variants.t: line 107: 26546 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 ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― Ok: 5 Expected Fail: 0 Fail: 0 Unexpected Pass: 0 Skipped: 0 Timeout: 0 Full log written to /build/freebayes-1.3.6/build/meson-logs/testlog.txt rm test/bash-tap/* rm test/test-simple-bash/* make[1]: Leaving directory '/build/freebayes-1.3.6' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson -O--builddir=build dh_prep -O--buildsystem=meson -O--builddir=build dh_auto_install --destdir=debian/freebayes/ -O--buildsystem=meson -O--builddir=build cd build && DESTDIR=/build/freebayes-1.3.6/debian/freebayes LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing freebayes to /build/freebayes-1.3.6/debian/freebayes/usr/bin Installing bamleftalign to /build/freebayes-1.3.6/debian/freebayes/usr/bin dh_install -O--buildsystem=meson -O--builddir=build dh_installdocs -O--buildsystem=meson -O--builddir=build dh_installchangelogs -O--buildsystem=meson -O--builddir=build dh_installexamples -O--buildsystem=meson -O--builddir=build dh_installsystemduser -O--buildsystem=meson -O--builddir=build dh_perl -O--buildsystem=meson -O--builddir=build dh_link -O--buildsystem=meson -O--builddir=build dh_strip_nondeterminism -O--buildsystem=meson -O--builddir=build dh_compress -O--buildsystem=meson -O--builddir=build dh_fixperms -O--buildsystem=meson -O--builddir=build dh_missing -O--buildsystem=meson -O--builddir=build dh_dwz -a -O--buildsystem=meson -O--builddir=build dh_strip -a -O--buildsystem=meson -O--builddir=build dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build dh_installdeb -O--buildsystem=meson -O--builddir=build dh_gencontrol -O--buildsystem=meson -O--builddir=build dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=meson -O--builddir=build dh_builddeb -O--buildsystem=meson -O--builddir=build dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.6-2_arm64.deb'. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.6-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../freebayes_1.3.6-2_arm64.buildinfo dpkg-genchanges --build=binary -O../freebayes_1.3.6-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/29651 and its subdirectories I: Current time: Sun May 19 23:15:17 -12 2024 I: pbuilder-time-stamp: 1716203717 Tue Apr 18 04:52:20 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Tue Apr 18 04:52:20 UTC 2023 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Tue Apr 18 04:57:14 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Tue Apr 18 04:57:15 UTC 2023 I: freebayes_1.3.6-2_arm64.changes: Format: 1.8 Date: Tue, 01 Nov 2022 14:38:51 +0100 Source: freebayes Binary: freebayes freebayes-dbgsym Architecture: arm64 Version: 1.3.6-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.6-2) unstable; urgency=medium . * install scripts (+ python3 dependency accordingly) * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: 420aaac82c305cc9afb07220bc44a80a60b69996 6442980 freebayes-dbgsym_1.3.6-2_arm64.deb cfc3d9e793b3936551377c1c5168920b7b46a32e 10015 freebayes_1.3.6-2_arm64.buildinfo 5d8fb953d5fba2db87782f144aa22d4acefa9cdf 1425564 freebayes_1.3.6-2_arm64.deb Checksums-Sha256: 51036e67e1e478d3fedbc5d07a536a053d07251dbe21719633314ad91458f77c 6442980 freebayes-dbgsym_1.3.6-2_arm64.deb c64fb63146af7cc9e3cca46277cbf468bef184412a111815ed6a884837bdaa44 10015 freebayes_1.3.6-2_arm64.buildinfo 890a1c4e1283a92f018ef83ca297cc63a19e487780beccd352050ec219be5eca 1425564 freebayes_1.3.6-2_arm64.deb Files: a1961994442f87093ce320ce52d95a8d 6442980 debug optional freebayes-dbgsym_1.3.6-2_arm64.deb 1d282539d98671ed4fbaf19c02477eea 10015 science optional freebayes_1.3.6-2_arm64.buildinfo a6293b983efa80b8f3edd145e3993167 1425564 science optional freebayes_1.3.6-2_arm64.deb Tue Apr 18 04:57:17 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.e95NGE8P/freebayes_1.3.6-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.e95NGE8P/freebayes_1.3.6-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.e95NGE8P/freebayes_1.3.6-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.e95NGE8P/b1/freebayes_1.3.6-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.e95NGE8P/b2/freebayes_1.3.6-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.409s) 0.409s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.094s) 0.094s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue Apr 18 04:57:18 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 18 04:57:18 UTC 2023 I: freebayes from bookworm built successfully and reproducibly on arm64. Tue Apr 18 04:57:20 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 18 04:57:20 UTC 2023 I: Submitting 12K b1/freebayes_1.3.6-2_arm64.buildinfo.asc Tue Apr 18 04:57:22 UTC 2023 I: Submitting 12K b2/freebayes_1.3.6-2_arm64.buildinfo.asc Tue Apr 18 04:57:23 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 18 04:57:23 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 18 04:57:23 UTC 2023 I: Removing signed freebayes_1.3.6-2_arm64.buildinfo.asc files: removed './b1/freebayes_1.3.6-2_arm64.buildinfo.asc' removed './b2/freebayes_1.3.6-2_arm64.buildinfo.asc'