Start: 2026-11-12 04:46:29 GMT [testing] Package: libbio-samtools-perl Source: libbio-samtools-perl (1.43-5) Version: 1.43-5+b2 Installed-Size: 588 Maintainer: Debian Perl Group Architecture: amd64 Depends: perl (>= 5.42.2-3), perlapi-5.42.2, libc6 (>= 2.34), zlib1g (>= 1:1.2.3.4), libbio-perl-perl Enhances: gbrowse, samtools Description: Perl interface to SamTools library for DNA sequencing Homepage: https://metacpan.org/release/Bio-SamTools Description-md5: 73b654c3e7ee8120b5c9b0a3c60da326 Tag: devel::lang:perl, devel::library, implemented-in::c, implemented-in::perl, role::devel-lib, role::shared-lib Section: perl Priority: optional Filename: pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.43-5+b2_amd64.deb Size: 182088 MD5sum: ced1c4a0d1b775a78944e1caebbb4298 SHA256: d3a81da6c1445c8d6c0a46f1253d4199fbd06a374896b593361ad353003e6b70 [sid] Package: libbio-samtools-perl Source: libbio-samtools-perl (1.43-5) Version: 1.43-5+b3 Installed-Size: 584 Maintainer: Debian Perl Group Architecture: amd64 Depends: perl (>= 5.44.0-3), perlapi-5.44.0, libc6 (>= 2.34), zlib1g (>= 1:1.2.3.4), libbio-perl-perl Enhances: gbrowse, samtools Description: Perl interface to SamTools library for DNA sequencing Homepage: https://metacpan.org/release/Bio-SamTools Description-md5: 73b654c3e7ee8120b5c9b0a3c60da326 Tag: devel::lang:perl, devel::library, implemented-in::c, implemented-in::perl, role::devel-lib, role::shared-lib Section: perl Priority: optional Filename: pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.43-5+b3_amd64.deb Size: 181280 MD5sum: 2dab4daa4c514463ba45281b0dab601f SHA256: 49205f24c5d5614ca92d94c323f588ef56d89b6479bf7bec69f3f1b88d0a2dc1 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libbio-samtools-perl=1.43-5+b3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202608291513~1.6.0-23-g1172a6e5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libbio-samtools-perl=1.43-5+b3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.12.116+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.116-1 (2026-11-07) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpdth3h383 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpdth3h383 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdth3h383', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdth3h383', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdth3h383/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdth3h383/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/12', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/12', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpdth3h383/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'update'] 0m3.7s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [151 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6714 kB] Fetched 17.0 MB in 2s (8694 kB/s) Reading package lists... 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'update'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-yf', 'dist-upgrade'] 0m5.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash gcc-16-base libcap2 libgcc-s1 libstdc++6 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2546 kB of archives. After this operation, 2048 B disk space will be freed. Get:1 http://deb.debian.org/debian forky/main amd64 bash amd64 5.3-4+b1 [1581 kB] Get:2 http://deb.debian.org/debian forky/main amd64 gcc-16-base amd64 16.2.0-4 [39.3 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 16.2.0-4 [822 kB] Get:4 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 16.2.0-4 [74.1 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libcap2 amd64 1:2.78-1+b2 [28.9 kB] Fetched 2546 kB in 0s (29.9 MB/s) (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 ... 4956 files and directories currently installed.) Preparing to unpack .../bash_5.3-4+b1_amd64.deb ... Unpacking bash (5.3-4+b1) over (5.3-4) ... Setting up bash (5.3-4+b1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 4957 files and directories currently installed.) Preparing to unpack .../gcc-16-base_16.2.0-4_amd64.deb ... Unpacking gcc-16-base:amd64 (16.2.0-4) over (16.2.0-3) ... Setting up gcc-16-base:amd64 (16.2.0-4) ... (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 ... 4957 files and directories currently installed.) Preparing to unpack .../libstdc++6_16.2.0-4_amd64.deb ... Unpacking libstdc++6:amd64 (16.2.0-4) over (16.2.0-3) ... Setting up libstdc++6:amd64 (16.2.0-4) ... (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 ... 4957 files and directories currently installed.) Preparing to unpack .../libgcc-s1_16.2.0-4_amd64.deb ... Unpacking libgcc-s1:amd64 (16.2.0-4) over (16.2.0-3) ... Setting up libgcc-s1:amd64 (16.2.0-4) ... (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 ... 4957 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.78-1+b2_amd64.deb ... Unpacking libcap2:amd64 (1:2.78-1+b2) over (1:2.78-1+b1) ... Setting up libcap2:amd64 (1:2.78-1+b2) ... Processing triggers for debianutils (5.24) ... Processing triggers for libc-bin (2.43-7) ... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-yf', 'dist-upgrade'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.9s DUMP: e6952985bc549df0991e8b6d6d565a22 - 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.9s INFO: Running scripts post_setup 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_dummy_users'] 0m6.6s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_dummy_users'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_forbid_home'] 0m6.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_forbid_home'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_minimize'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_minimize'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_zz_backports'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_setup_zz_backports'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.6s DUMP: install ok installed apt apt 3.3.6 install ok installed base-files base-files 14.2 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-4+b1 install ok installed bsdutils bsdutils 1:2.42.4-1 install ok installed coreutils coreutils 9.12-0.3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.24 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.11 install ok installed findutils findutils 4.11.0-3 install ok installed gcc-16-base:amd64 gcc-16-base 16.2.0-4 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.14-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69+nmu3 install ok installed libacl1:amd64 libacl1 2.4.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.3.6 install ok installed libattr1:amd64 libattr1 1:2.6.0-1 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b2 install ok installed libblkid1:amd64 libblkid1 2.42.4-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b2 install ok installed libc-bin libc-bin 2.43-7 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.43-7 install ok installed libc6:amd64 libc6 2.43-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.6-1+b1 install ok installed libcap2:amd64 libcap2 1:2.78-1+b2 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.2+20251210-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-12 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.283 install ok installed libgcc-s1:amd64 libgcc-s1 16.2.0-4 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-10 install ok installed liblzma5:amd64 liblzma5 5.8.4-1 install ok installed libmd0:amd64 libmd0 1.3.0-1 install ok installed libmount1:amd64 libmount1 2.42.4-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-8 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-8 install ok installed libpam-runtime libpam-runtime 1.7.0-8 install ok installed libpam0g:amd64 libpam0g 1.7.0-8 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.49-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.1-1+b2 install ok installed libselinux1:amd64 libselinux1 3.11-2.1+b1 install ok installed libsemanage-common libsemanage-common 3.11-1 install ok installed libsemanage2:amd64 libsemanage2 3.11-1+b2 install ok installed libsepol2:amd64 libsepol2 3.11-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.42.4-1 install ok installed libssl3t64:amd64 libssl3t64 3.6.5-1 install ok installed libstdc++6:amd64 libstdc++6 16.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 262-1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20260608-2 install ok installed libudev1:amd64 libudev1 262-1 install ok installed libuuid1:amd64 libuuid1 2.42.4-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-4 install ok installed login login 1:4.16.0-2+really2.42.4-1 install ok installed login.defs login.defs 1:4.20.3-1 install ok installed mawk mawk 1.3.4.20260302-2 install ok installed mount mount 2.42.4-1 install ok installed ncurses-base ncurses-base 6.6+20260608-2 install ok installed ncurses-bin ncurses-bin 6.6+20260608-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.6.5-1 install ok installed passwd passwd 1:4.20.3-1 install ok installed perl-base perl-base 5.42.3-1 install ok installed sed sed 4.9-3 install ok installed sqv sqv 1.5.0-1 install ok installed sysvinit-utils sysvinit-utils 3.18-1 install ok installed tar tar 1.35+dfsg-7 install ok installed tzdata tzdata 2026f-1 install ok installed util-linux util-linux 2.42.4-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.2-4 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m6.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m7.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m7.0s INFO: Running scripts is_testable 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/is_testable_uninstallable'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/is_testable_uninstallable'] 0m7.0s INFO: Running scripts pre_test 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_test_exceptions'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_test_exceptions'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_test_root_password'] 0m7.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_test_root_password'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'show', '--no-all-versions', 'libbio-samtools-perl'] 0m7.6s DUMP: Package: libbio-samtools-perl Source: libbio-samtools-perl (1.43-5) Version: 1.43-5+b2 Installed-Size: 588 Maintainer: Debian Perl Group Architecture: amd64 Depends: perl (>= 5.42.2-3), perlapi-5.42.2, libc6 (>= 2.34), zlib1g (>= 1:1.2.3.4), libbio-perl-perl Enhances: gbrowse, samtools Description-en: Perl interface to SamTools library for DNA sequencing Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application. Description-md5: 73b654c3e7ee8120b5c9b0a3c60da326 Homepage: https://metacpan.org/release/Bio-SamTools Tag: devel::lang:perl, devel::library, implemented-in::c, implemented-in::perl, role::devel-lib, role::shared-lib Section: perl Priority: optional Filename: pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.43-5+b2_amd64.deb Size: 182088 MD5sum: ced1c4a0d1b775a78944e1caebbb4298 SHA256: d3a81da6c1445c8d6c0a46f1253d4199fbd06a374896b593361ad353003e6b70 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'show', '--no-all-versions', 'libbio-samtools-perl'] 0m7.6s INFO: apt-cache knows about the following packages: libbio-samtools-perl 0m7.6s INFO: Running scripts pre_install 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_database-server'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_database-server'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_exceptions'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_exceptions'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_extras'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_extras'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy'] 0m7.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m7.8s DUMP: libbio-samtools-perl: Installed: (none) Candidate: 1.43-5+b2 Version table: 1.43-5+b2 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-y', 'install', 'libbio-samtools-perl'] 0m10.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: libbio-perl-perl libdata-stag-perl libgdbm-compat4t64 libgdbm6t64 libio-string-perl libperl5.42 perl perl-modules-5.42 Suggested packages: bioperl libxml-sax-expatxs-perl libbio-alignio-stockholm-perl gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl Recommended packages: bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl libgd-perl libmldbm-perl libxml-libxslt-perl libxml-perl perl-tk netbase The following NEW packages will be installed: libbio-perl-perl libbio-samtools-perl libdata-stag-perl libgdbm-compat4t64 libgdbm6t64 libio-string-perl libperl5.42 perl perl-modules-5.42 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After this operation, 59.4 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 perl-modules-5.42 all 5.42.3-1 [3213 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libgdbm6t64 amd64 1.26-1+b2 [77.7 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libgdbm-compat4t64 amd64 1.26-1+b2 [52.0 kB] Get:4 http://deb.debian.org/debian forky/main amd64 libperl5.42 amd64 5.42.3-1 [4272 kB] Get:5 http://deb.debian.org/debian forky/main amd64 perl amd64 5.42.3-1 [266 kB] Get:6 http://deb.debian.org/debian forky/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libdata-stag-perl all 0.14-4 [440 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libbio-perl-perl all 1.7.8-4 [2498 kB] Get:9 http://deb.debian.org/debian forky/main amd64 libbio-samtools-perl amd64 1.43-5+b2 [182 kB] Fetched 11.0 MB in 0s (86.8 MB/s) Selecting previously unselected package perl-modules-5.42. (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 ... 4961 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.42_5.42.3-1_all.deb ... Unpacking perl-modules-5.42 (5.42.3-1) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.26-1+b2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.26-1+b2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../2-libgdbm-compat4t64_1.26-1+b2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.26-1+b2) ... Selecting previously unselected package libperl5.42:amd64. Preparing to unpack .../3-libperl5.42_5.42.3-1_amd64.deb ... Unpacking libperl5.42:amd64 (5.42.3-1) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.42.3-1_amd64.deb ... Unpacking perl (5.42.3-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../5-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../6-libdata-stag-perl_0.14-4_all.deb ... Unpacking libdata-stag-perl (0.14-4) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../7-libbio-perl-perl_1.7.8-4_all.deb ... Unpacking libbio-perl-perl (1.7.8-4) ... Selecting previously unselected package libbio-samtools-perl. Preparing to unpack .../8-libbio-samtools-perl_1.43-5+b2_amd64.deb ... Unpacking libbio-samtools-perl (1.43-5+b2) ... Setting up libgdbm6t64:amd64 (1.26-1+b2) ... Setting up libgdbm-compat4t64:amd64 (1.26-1+b2) ... Setting up perl-modules-5.42 (5.42.3-1) ... Setting up libperl5.42:amd64 (5.42.3-1) ... Setting up perl (5.42.3-1) ... Setting up libio-string-perl (1.08-4) ... Setting up libdata-stag-perl (0.14-4) ... Setting up libbio-perl-perl (1.7.8-4) ... Setting up libbio-samtools-perl (1.43-5+b2) ... Processing triggers for libc-bin (2.43-7) ... 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-y', 'install', 'libbio-samtools-perl'] 0m10.3s INFO: Running scripts post_install 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_install_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_install_exceptions'] 0m10.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m10.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m10.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpdth3h383 to sid 0m10.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m10.7s INFO: Running scripts pre_distupgrade 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'update'] 0m13.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [193 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.9 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7788 kB] Fetched 18.8 MB in 2s (8443 kB/s) Reading package lists... 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'update'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-yf', 'dist-upgrade'] 0m17.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: libperl5.42 perl-modules-5.42 The following NEW packages will be installed: libperl5.44 perl-modules-5.44 The following packages will be upgraded: apt libapt-pkg7.0 libaudit-common libaudit1 libbio-samtools-perl libsystemd0 libudev1 perl perl-base sysvinit-utils 10 upgraded, 2 newly installed, 2 to remove and 0 not upgraded. Need to get 13.6 MB of archives. After this operation, 1292 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libbio-samtools-perl amd64 1.43-5+b3 [181 kB] Get:2 http://deb.debian.org/debian sid/main amd64 perl-modules-5.44 all 5.44.0-3 [3261 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libperl5.44 amd64 5.44.0-3 [4354 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl amd64 5.44.0-3 [266 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.44.0-3 [1921 kB] Get:6 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.18-2 [29.9 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 262.2-1 [513 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 262.2-1 [149 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.3.7 [1293 kB] Get:10 http://deb.debian.org/debian sid/main amd64 apt amd64 3.3.7 [1580 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.2.1-1 [13.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.2.1-1+b1 [59.9 kB] Fetched 13.6 MB in 0s (83.5 MB/s) (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 ... 8410 files and directories currently installed.) Preparing to unpack .../libbio-samtools-perl_1.43-5+b3_amd64.deb ... Unpacking libbio-samtools-perl (1.43-5+b3) over (1.43-5+b2) ... Preparing to unpack .../perl_5.44.0-3_amd64.deb ... Unpacking perl (5.44.0-3) over (5.42.3-1) ... Selecting previously unselected package perl-modules-5.44. Preparing to unpack .../perl-modules-5.44_5.44.0-3_all.deb ... Unpacking perl-modules-5.44 (5.44.0-3) ... Selecting previously unselected package libperl5.44:amd64. Preparing to unpack .../libperl5.44_5.44.0-3_amd64.deb ... Unpacking libperl5.44:amd64 (5.44.0-3) ... Preparing to unpack .../perl-base_5.44.0-3_amd64.deb ... Unpacking perl-base (5.44.0-3) over (5.42.3-1) ... Setting up perl-base (5.44.0-3) ... (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 ... 10593 files and directories currently installed.) Removing libperl5.42:amd64 (5.42.3-1) ... Removing perl-modules-5.42 (5.42.3-1) ... (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 ... 8443 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.18-2_amd64.deb ... Unpacking sysvinit-utils (3.18-2) over (3.18-1) ... Setting up sysvinit-utils (3.18-2) ... (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 ... 8443 files and directories currently installed.) Preparing to unpack .../libsystemd0_262.2-1_amd64.deb ... Unpacking libsystemd0:amd64 (262.2-1) over (262-1) ... Setting up libsystemd0:amd64 (262.2-1) ... (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 ... 8443 files and directories currently installed.) Preparing to unpack .../libudev1_262.2-1_amd64.deb ... Unpacking libudev1:amd64 (262.2-1) over (262-1) ... Setting up libudev1:amd64 (262.2-1) ... (Reading database ... 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(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 ... 8443 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.2.1-1+b1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.2.1-1+b1) over (1:4.1.2-1+b2) ... Setting up libaudit1:amd64 (1:4.2.1-1+b1) ... Setting up perl-modules-5.44 (5.44.0-3) ... Setting up libperl5.44:amd64 (5.44.0-3) ... Setting up perl (5.44.0-3) ... Setting up libbio-samtools-perl (1.43-5+b3) ... Processing triggers for libc-bin (2.43-7) ... 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-yf', 'dist-upgrade'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.9s DUMP: 179968a04445472ccd88b99023f765ba - 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'show', '--no-all-versions', 'libbio-samtools-perl'] 0m19.2s DUMP: Package: libbio-samtools-perl Source: libbio-samtools-perl (1.43-5) Version: 1.43-5+b3 Installed-Size: 584 Maintainer: Debian Perl Group Architecture: amd64 Depends: perl (>= 5.44.0-3), perlapi-5.44.0, libc6 (>= 2.34), zlib1g (>= 1:1.2.3.4), libbio-perl-perl Enhances: gbrowse, samtools Description-en: Perl interface to SamTools library for DNA sequencing Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application. Description-md5: 73b654c3e7ee8120b5c9b0a3c60da326 Homepage: https://metacpan.org/release/Bio-SamTools Tag: devel::lang:perl, devel::library, implemented-in::c, implemented-in::perl, role::devel-lib, role::shared-lib Section: perl Priority: optional Filename: pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.43-5+b3_amd64.deb Size: 181280 MD5sum: 2dab4daa4c514463ba45281b0dab601f SHA256: 49205f24c5d5614ca92d94c323f588ef56d89b6479bf7bec69f3f1b88d0a2dc1 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'show', '--no-all-versions', 'libbio-samtools-perl'] 0m19.2s INFO: apt-cache knows about the following packages: libbio-samtools-perl 0m19.2s INFO: Running scripts pre_install 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_database-server'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_database-server'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_exceptions'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_extras'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_extras'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy'] 0m19.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m19.3s DUMP: libbio-samtools-perl: Installed: 1.43-5+b3 Candidate: 1.43-5+b3 Version table: *** 1.43-5+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-y', 'install', 'libbio-samtools-perl'] 0m20.0s DUMP: Reading package lists... Building dependency tree... Reading state information... libbio-samtools-perl is already the newest version (1.43-5+b3). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-y', 'install', 'libbio-samtools-perl'] 0m20.0s INFO: Running scripts post_install 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_install_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_install_exceptions'] 0m20.0s INFO: Running scripts post_distupgrade 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_exceptions'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_zz_backports'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_distupgrade_zz_backports'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m20.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m20.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m21.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m21.1s INFO: Running scripts pre_install 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_database-server'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_database-server'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_exceptions'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_extras'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_extras'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy'] 0m21.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m21.2s DUMP: libbio-samtools-perl: Installed: 1.43-5+b3 Candidate: 1.43-5+b3 Version table: *** 1.43-5+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-y', 'install', 'libbio-samtools-perl=1.43-5+b3'] 0m22.0s DUMP: Reading package lists... Building dependency tree... Reading state information... libbio-samtools-perl is already the newest version (1.43-5+b3). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', '-y', 'install', 'libbio-samtools-perl=1.43-5+b3'] 0m22.0s INFO: Running scripts post_install 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_install_exceptions'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_install_exceptions'] 0m22.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m22.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m22.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdth3h383', '-ac', '--ignore-obsolete'] 0m23.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdth3h383', '-ac', '--ignore-obsolete'] 0m23.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.7s DUMP: 0.17.5+b5 0m23.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.7s INFO: Running adequate version 0.17.5+b5 now. 0m23.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'libbio-samtools-perl'] 0m23.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'libbio-samtools-perl'] 0m23.8s INFO: Running scripts pre_remove 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_exceptions'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/pre_remove_exceptions'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.3s DUMP: install ok installed apt apt 3.3.7 install ok installed base-files base-files 14.2 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-4+b1 install ok installed bsdutils bsdutils 1:2.42.4-1 install ok installed coreutils coreutils 9.12-0.3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.24 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.11 install ok installed findutils findutils 4.11.0-3 install ok installed gcc-16-base:amd64 gcc-16-base 16.2.0-4 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.14-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69+nmu3 install ok installed libacl1:amd64 libacl1 2.4.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.3.7 install ok installed libattr1:amd64 libattr1 1:2.6.0-1 install ok installed libaudit-common libaudit-common 1:4.2.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.2.1-1+b1 install ok installed libbio-perl-perl libbio-perl-perl 1.7.8-4 install ok installed libbio-samtools-perl libbio-samtools-perl 1.43-5+b3 install ok installed libblkid1:amd64 libblkid1 2.42.4-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b2 install ok installed libc-bin libc-bin 2.43-7 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.43-7 install ok installed libc6:amd64 libc6 2.43-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.6-1+b1 install ok installed libcap2:amd64 libcap2 1:2.78-1+b2 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.2+20251210-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-12 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.283 install ok installed libgcc-s1:amd64 libgcc-s1 16.2.0-4 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.26-1+b2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.26-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1+b1 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-10 install ok installed liblzma5:amd64 liblzma5 5.8.4-1 install ok installed libmd0:amd64 libmd0 1.3.0-1 install ok installed libmount1:amd64 libmount1 2.42.4-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-8 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-8 install ok installed libpam-runtime libpam-runtime 1.7.0-8 install ok installed libpam0g:amd64 libpam0g 1.7.0-8 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.49-1 install ok installed libperl5.44:amd64 libperl5.44 5.44.0-3 install ok installed libseccomp2:amd64 libseccomp2 2.6.1-1+b2 install ok installed libselinux1:amd64 libselinux1 3.11-2.1+b1 install ok installed libsemanage-common libsemanage-common 3.11-1 install ok installed libsemanage2:amd64 libsemanage2 3.11-1+b2 install ok installed libsepol2:amd64 libsepol2 3.11-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.42.4-1 install ok installed libssl3t64:amd64 libssl3t64 3.6.5-1 install ok installed libstdc++6:amd64 libstdc++6 16.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 262.2-1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20260608-2 install ok installed libudev1:amd64 libudev1 262.2-1 install ok installed libuuid1:amd64 libuuid1 2.42.4-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-4 install ok installed login login 1:4.16.0-2+really2.42.4-1 install ok installed login.defs login.defs 1:4.20.3-1 install ok installed mawk mawk 1.3.4.20260302-2 install ok installed mount mount 2.42.4-1 install ok installed ncurses-base ncurses-base 6.6+20260608-2 install ok installed ncurses-bin ncurses-bin 6.6+20260608-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.6.5-1 install ok installed passwd passwd 1:4.20.3-1 install ok installed perl perl 5.44.0-3 install ok installed perl-base perl-base 5.44.0-3 install ok installed perl-modules-5.44 perl-modules-5.44 5.44.0-3 install ok installed sed sed 4.9-3 install ok installed sqv sqv 1.5.0-1 install ok installed sysvinit-utils sysvinit-utils 3.18-2 install ok installed tar tar 1.35+dfsg-7 install ok installed tzdata tzdata 2026f-1 install ok installed util-linux util-linux 2.42.4-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.2-4 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'remove', '--allow-remove-essential', 'libbio-perl-perl', 'libdata-stag-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libio-string-perl', 'libperl5.44:amd64', 'perl', 'perl-modules-5.44', 'libbio-samtools-perl'] 0m25.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following packages will be REMOVED: libbio-perl-perl libbio-samtools-perl libdata-stag-perl libgdbm-compat4t64 libgdbm6t64 libio-string-perl libperl5.44 perl perl-modules-5.44 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. After this operation, 60.3 MB disk space will be freed. (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 ... 8443 files and directories currently installed.) Removing libbio-samtools-perl (1.43-5+b3) ... Removing libbio-perl-perl (1.7.8-4) ... Removing libdata-stag-perl (0.14-4) ... Removing libio-string-perl (1.08-4) ... Removing perl (5.44.0-3) ... Removing libperl5.44:amd64 (5.44.0-3) ... Removing libgdbm-compat4t64:amd64 (1.26-1+b2) ... Removing libgdbm6t64:amd64 (1.26-1+b2) ... Removing perl-modules-5.44 (5.44.0-3) ... Processing triggers for libc-bin (2.43-7) ... 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'remove', '--allow-remove-essential', 'libbio-perl-perl', 'libdata-stag-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libio-string-perl', 'libperl5.44:amd64', 'perl', 'perl-modules-5.44', 'libbio-samtools-perl'] 0m25.7s INFO: Running scripts post_remove 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_remove_exceptions'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_remove_exceptions'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--purge', 'libbio-perl-perl', 'libdata-stag-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libio-string-perl', 'libperl5.44:amd64', 'perl', 'perl-modules-5.44'] 0m25.7s DUMP: dpkg: warning: ignoring request to remove libbio-perl-perl which is not installed dpkg: warning: ignoring request to remove libdata-stag-perl which is not installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which is not installed dpkg: warning: ignoring request to remove libgdbm6t64 which is not installed dpkg: warning: ignoring request to remove libio-string-perl which is not installed dpkg: warning: ignoring request to remove libperl5.44 which is not installed (Reading database ... 4978 files and directories currently installed.) Purging configuration files for perl (5.44.0-3) ... dpkg: warning: ignoring request to remove perl-modules-5.44 which is not installed 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--purge', 'libbio-perl-perl', 'libdata-stag-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libio-string-perl', 'libperl5.44:amd64', 'perl', 'perl-modules-5.44'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--purge', 'libbio-samtools-perl'] 0m25.7s DUMP: dpkg: warning: ignoring request to remove libbio-samtools-perl which is not installed 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--purge', 'libbio-samtools-perl'] 0m25.7s INFO: Running scripts post_purge 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_purge_exceptions'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_purge_exceptions'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--purge', '--pending'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--purge', '--pending'] 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--remove', '--pending'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg', '--remove', '--pending'] 0m25.8s INFO: Running scripts post_test 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_test_exceptions'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'tmp/scripts/post_test_exceptions'] 0m25.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m26.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg-divert', '--list'] 0m26.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m26.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'dpkg-divert', '--list'] 0m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'clean'] 0m26.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdth3h383', 'apt-get', 'clean'] 0m26.1s DEBUG: Recording chroot state 0m27.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/shm'] 0m27.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/shm'] 0m27.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/console'] 0m27.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/console'] 0m27.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/ptmx'] 0m27.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/ptmx'] 0m27.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/pts'] 0m27.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/dev/pts'] 0m27.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/proc'] 0m27.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdth3h383/proc'] 0m27.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m27.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdth3h383'] 0m27.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpdth3h383 0m27.4s INFO: PASS: Upgrading between Debian distributions. 0m27.4s INFO: PASS: All tests. 0m27.4s INFO: piuparts run ends. ret=0 End: 2026-11-12 04:46:57 GMT