Start: 2024-10-11 15:15:28 GMT Package: srst2 Version: 0.2.0-12 Installed-Size: 265 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, bowtie2, cd-hit, samtools, python3-scipy, python3-biopython Recommends: python3-rpy2 Description: Short Read Sequence Typing for Bacterial Pathogens Homepage: https://katholt.github.io/srst2/ Description-md5: 0b05e0f1dc4b9a9dedc867def03c95b1 Section: science Priority: optional Filename: pool/main/s/srst2/srst2_0.2.0-12_amd64.deb Size: 61224 MD5sum: c07b6de6ccdd564e0ed872cc0e618440 SHA256: 8eeb1cfc934395484c45ce84ea94ee24d227cc4c0c4f726678d49e29b3da288f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-no-usr-share-doc --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt srst2=0.2.0-12 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-no-usr-share-doc --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt srst2=0.2.0-12 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmprh2ub7uj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmprh2ub7uj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmprh2ub7uj/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-no-usr-share-doc to /srv/piuparts.debian.org/tmp/tmprh2ub7uj/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'update'] 0m3.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7337 kB] Fetched 17.5 MB in 2s (8008 kB/s) Reading package lists... 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'update'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', '-yf', 'dist-upgrade'] 0m4.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: hostname 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.25 [11.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.0 kB in 0s (521 kB/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 ... 5127 files and directories currently installed.) Preparing to unpack .../hostname_3.25_amd64.deb ... Unpacking hostname (3.25) over (3.24) ... Setting up hostname (3.25) ... 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', '-yf', 'dist-upgrade'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s DUMP: a8437af785428afa3d3475ef570d60ba - 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s INFO: Running scripts post_setup 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_disable_usr_share_doc'] 0m4.6s DUMP: dpkg-query: no packages found matching systemd-sysv dpkg-query: no packages found matching sysv-rc 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_disable_usr_share_doc'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s 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 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s 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' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'clean'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'clean'] 0m5.4s DEBUG: Recording chroot state 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.8s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b1 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-6 install ok installed gpgv gpgv 2.2.44-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 256.7-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.7-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.38.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-divert', '--list'] 0m5.8s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 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 /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 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 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-divert', '--list'] 0m5.8s INFO: Running scripts is_testable 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s INFO: apt-cache does not know about any of the requested packages 0m5.9s INFO: Running scripts pre_test 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_test_root_password'] 0m5.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_test_root_password'] 0m5.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 0m6.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 0m6.6s DEBUG: No broken symlinks as far as we can find. 0m6.6s INFO: Running scripts pre_install 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 0m7.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 0m7.5s DEBUG: No broken symlinks as far as we can find. 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-cache', 'policy'] 0m8.2s 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: 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-cache', 'policy'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-cache', 'policy', 'srst2'] 0m8.3s DUMP: srst2: Installed: (none) Candidate: 0.2.0-12 Version table: 0.2.0-12 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-cache', 'policy', 'srst2'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', '-y', 'install', 'srst2=0.2.0-12'] 1m2.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bowtie2 cd-hit fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libperl5.38t64 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtiff6 libtirpc-common libtirpc3t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase perl perl-modules-5.38 python3 python3-autocommand python3-biopython python3-cairo python3-chardet python3-decorator python3-freetype python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3-scipy python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gdbm-l10n low-memory-monitor krb5-doc krb5-user liblcms2-utils sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3.12-venv python3.12-doc binutils binfmt-support readline-doc cwltool sgml-base-doc debhelper Recommended packages: ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-rpy2 The following NEW packages will be installed: bowtie2 cd-hit fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libperl5.38t64 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtiff6 libtirpc-common libtirpc3t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase perl perl-modules-5.38 python3 python3-autocommand python3-biopython python3-cairo python3-chardet python3-decorator python3-freetype python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3-scipy python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools sgml-base srst2 w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 70.3 MB of archives. After this operation, 270 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-5 [2905 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-5 [4275 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-5 [236 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.7-1 [814 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.7-1 [2162 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:10 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:11 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:16 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:21 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.7-1 [1965 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.7-1 [671 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:27 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:28 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:29 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.4-1 [1510 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-6 [137 kB] Get:31 http://deb.debian.org/debian sid/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:32 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:33 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:38 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:39 http://deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:40 http://deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:41 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:42 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-6 [9284 B] Get:44 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:57 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[167 kB] Get:79 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:80 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:81 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:82 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get:91 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:92 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:93 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:94 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:95 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:96 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:97 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:98 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:99 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:100 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:101 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.26.1-2 [114 kB] Get:103 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:105 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get:106 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:107 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:108 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.84+dfsg-2 [1645 kB] Get:109 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.13.1-5 [16.7 MB] Get:111 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.20-3 [653 kB] Get:112 http://deb.debian.org/debian sid/main amd64 srst2 amd64 0.2.0-12 [61.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.3 MB in 1s (89.5 MB/s) Selecting previously unselected package perl-modules-5.38. (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 ... 5131 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.38_5.38.2-5_all.deb ... Unpacking perl-modules-5.38 (5.38.2-5) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. 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Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7468 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... 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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 ... 8025 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package bowtie2. Preparing to unpack .../02-bowtie2_2.5.4-1_amd64.deb ... Unpacking bowtie2 (2.5.4-1) ... 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Preparing to unpack .../84-samtools_1.20-3_amd64.deb ... Unpacking samtools (1.20-3) ... Selecting previously unselected package srst2. Preparing to unpack .../85-srst2_0.2.0-12_amd64.deb ... Unpacking srst2 (0.2.0-12) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libgomp1:amd64 (14.2.0-6) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up perl-modules-5.38 (5.38.2-5) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libatomic1:amd64 (14.2.0-6) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-6) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libperl5.38t64:amd64 (5.38.2-5) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up readline-common (8.2-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up perl (5.38.2-5) ... Setting up libglib2.0-0t64:amd64 (2.82.1-1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up cd-hit (4.8.1-4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-1) ... Setting up python3.12 (3.12.7-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... /usr/share/srst2/database_clustering/VFDB_cdhit_to_csv.py:53: SyntaxWarning: invalid escape sequence '\(' in_brackets = re.findall('\((.*?)\)', full_name) /usr/share/srst2/database_clustering/align_plot_tree_min3.py:28: SyntaxWarning: invalid escape sequence '\.' r(''' /usr/share/srst2/getmlst.py:181: SyntaxWarning: invalid escape sequence '\d' m = re.match('>(.*)([_-])(\d*)',head).groups() /usr/share/srst2/srst2.py:90: SyntaxWarning: invalid escape sequence '\-' parser.add_argument('--other', type=str, help='Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".', required=False) /usr/share/srst2/srst2.py:99: SyntaxWarning: invalid escape sequence '\-' parser.add_argument('--samtools_args', type=str, help='Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").', required=False) /usr/share/srst2/srst2.py:241: SyntaxWarning: invalid escape sequence '\d' m = re.search("NM:i:(\d+)\s",line) Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up bowtie2 (2.5.4-1) ... Setting up python3-pil:amd64 (10.4.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-cairo (1.26.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-scipy (1.13.1-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-2) ... Setting up srst2 (0.2.0-12) ... 1m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', '-y', 'install', 'srst2=0.2.0-12'] 1m2.3s INFO: Running scripts post_install 1m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_install_exceptions'] 1m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_install_exceptions'] 1m2.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 1m3.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 1m5.0s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-ExtraLight.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuMathTeXGyre.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuMathTeXGyre.ttf (python3-reportlab) /usr/share/doc/python3.12/python-policy.txt.gz -> ../python3/python-policy.txt.gz (python3) /usr/share/doc/python3.12/changelog.gz -> NEWS.gz (python3.12) /usr/share/doc/perl/Changes.gz -> changelog.gz (perl) 1m5.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', '-ac', '--ignore-obsolete'] 1m7.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', '-ac', '--ignore-obsolete'] 1m7.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m7.8s DUMP: 0.15.6 1m7.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m7.8s INFO: Running adequate version 0.15.6 now. 1m7.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'srst2'] 1m7.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'srst2'] 1m7.9s INFO: Running scripts pre_remove 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_exceptions'] 1m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/pre_remove_exceptions'] 1m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m9.9s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b1 install ok installed bowtie2 bowtie2 2.5.4-1 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-6 install ok installed gpgv gpgv 2.2.44-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libatomic1:amd64 libatomic1 14.2.0-6 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.10.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.3-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-6 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.1-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 9.0.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libncurses6:amd64 libncurses6 6.5-2 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.63.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-5 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-1 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-7 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 256.7-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libudev1:amd64 libudev1 256.7-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1+b1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1+b1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2 install ok installed libxcb1:amd64 libxcb1 1.17.0-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.38.2-5 install ok installed perl-base perl-base 5.38.2-5 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-5 install ok installed python3 python3 3.12.6-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.84+dfsg-2 install ok installed python3-cairo python3-cairo 1.26.1-2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 install ok installed python3-pil:amd64 python3-pil 10.4.0-1 install ok installed python3-pkg-resources python3-pkg-resources 74.1.2-2 install ok installed python3-reportlab python3-reportlab 4.2.5-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.13.1-5 install ok installed python3-typeguard python3-typeguard 4.3.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3.12 python3.12 3.12.7-1 install ok installed python3.12-minimal python3.12-minimal 3.12.7-1 install ok installed readline-common readline-common 8.2-5 install ok installed samtools samtools 1.20-3 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed srst2 srst2 0.2.0-12 install ok installed sysvinit-utils sysvinit-utils 3.10-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 1m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'remove', 'bowtie2', 'cd-hit', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'srst2'] 1m47.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bowtie2 cd-hit fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libperl5.38t64 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtiff6 libtirpc-common libtirpc3t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase perl perl-modules-5.38 python3 python3-autocommand python3-biopython python3-cairo python3-chardet python3-decorator python3-freetype python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3-scipy python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools sgml-base srst2 w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 112 to remove and 0 not upgraded. After this operation, 270 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 ... 13743 files and directories currently installed.) Removing srst2 (0.2.0-12) ... Removing bowtie2 (2.5.4-1) ... Removing cd-hit (4.8.1-4) ... Removing python3-biopython (1.84+dfsg-2) ... Removing python3-reportlab (4.2.5-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-urw-base35 (20200910-8) ... Removing python3-pil:amd64 (10.4.0-1) ... Removing libraqm0:amd64 (0.10.1-1+b1) ... Removing libharfbuzz0b:amd64 (9.0.0-1) ... Removing libglib2.0-0t64:amd64 (2.82.1-1) ... Removing libatomic1:amd64 (14.2.0-6) ... Removing python3-scipy (1.13.1-5) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing samtools (1.20-3) ... Removing libhts3t64:amd64 (1.20+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.10.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-pkg-resources (74.1.2-2) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.3.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing libfontenc1:amd64 (1:1.1.8-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing perl (5.38.2-5) ... Removing libperl5.38t64:amd64 (5.38.2-5) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-6) ... Removing libimagequant0:amd64 (2.18.0-1+b1) ... Removing libgomp1:amd64 (14.2.0-6) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libncurses6:amd64 (6.5-2) ... Removing libnghttp2-14:amd64 (1.63.0-1) ... Removing libnghttp3-9:amd64 (1.4.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b3) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libwebpmux3:amd64 (1.4.0-0.1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1) ... Removing libwebp7:amd64 (1.4.0-0.1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.0-7) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libx11-6:amd64 (2:1.8.7-1+b1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxcb-shm0:amd64 (1.17.0-2) ... Removing libxcb-render0:amd64 (1.17.0-2) ... Removing libxcb1:amd64 (1.17.0-2) ... Removing libxau6:amd64 (1:1.0.9-1+b1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b1) ... Removing perl-modules-5.38 (5.38.2-5) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing python3 (3.12.6-1) ... Removing python3.12 (3.12.7-1) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12-minimal (3.12.7-1) ... Removing libexpat1:amd64 (2.6.3-1) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2) ... Removing libpython3.12-minimal:amd64 (3.12.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 1m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'remove', 'bowtie2', 'cd-hit', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'srst2'] 1m47.0s INFO: Running scripts post_remove 1m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_remove_exceptions'] 1m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_remove_exceptions'] 1m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--purge', 'bowtie2', 'cd-hit', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m47.5s DUMP: dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove cd-hit which isn't installed (Reading database ... 5192 files and directories currently installed.) Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.1-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.38t64 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for perl (5.38.2-5) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for python3 (3.12.6-1) ... dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-1) ... Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 1m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--purge', 'bowtie2', 'cd-hit', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--purge', 'srst2'] 1m47.5s DUMP: dpkg: warning: ignoring request to remove srst2 which isn't installed 1m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--purge', 'srst2'] 1m47.5s INFO: Running scripts post_purge 1m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_purge_exceptions'] 1m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_purge_exceptions'] 1m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--purge', '--pending'] 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--purge', '--pending'] 1m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--remove', '--pending'] 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg', '--remove', '--pending'] 1m47.6s INFO: Running scripts post_test 1m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_test_exceptions'] 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'tmp/scripts/post_test_exceptions'] 1m47.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 1m47.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 1m48.3s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf 1m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-divert', '--list'] 1m48.3s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 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 /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 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 1m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'dpkg-divert', '--list'] 1m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'clean'] 1m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj', 'apt-get', 'clean'] 1m48.3s DEBUG: Recording chroot state 1m48.8s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 1m48.8s INFO: PASS: Installation and purging test. 1m49.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/shm'] 1m49.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/shm'] 1m49.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/console'] 1m49.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/console'] 1m49.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/ptmx'] 1m49.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/ptmx'] 1m49.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/pts'] 1m49.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/dev/pts'] 1m49.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/proc'] 1m49.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj/proc'] 1m49.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 1m49.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprh2ub7uj'] 1m49.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmprh2ub7uj 1m49.4s INFO: PASS: All tests. 1m49.4s INFO: piuparts run ends. ret=0 End: 2024-10-11 15:17:17 GMT