Start: 2024-12-02 21:20:06 GMT [testing] Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: http://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 [sid] Package: roary Version: 3.13.0+dfsg-2 Installed-Size: 732 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: https://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-2_all.deb Size: 185372 MD5sum: b9a0608203b4c68c800b0b143f644c54 SHA256: d17eb6670706c80adb047f608f299e09cad011f4d21f330036010db9152cd648 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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-2 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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt roary=3.13.0+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmp5bzj4fd0 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5bzj4fd0 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5bzj4fd0/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'update'] 0m1.8s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9343 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6269 kB] Fetched 15.8 MB in 1s (15.4 MB/s) Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libcap-ng0 libseccomp2 libsystemd0 libudev1 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 660 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257~rc3-1 [448 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257~rc3-1 [147 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 660 kB in 0s (32.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5150 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-4_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-4) over (0.8.5-3+b1) ... Setting up libcap-ng0:amd64 (0.8.5-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5149 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../libsystemd0_257~rc3-1_amd64.deb ... Unpacking libsystemd0:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libsystemd0:amd64 (257~rc3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../libudev1_257~rc3-1_amd64.deb ... Unpacking libudev1:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libudev1:amd64 (257~rc3-1) ... Processing triggers for libc-bin (2.40-3) ... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s DUMP: fa645469152ec28ae4a37a68a082c549 - 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s INFO: Running scripts post_setup 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s 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 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s 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' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 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 5.21 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+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 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+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 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 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s INFO: Running scripts pre_test 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m3.5s DUMP: Package: roary Version: 3.13.0+dfsg-1 Installed-Size: 670 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description-en: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. Description-md5: 6d457fd706202fc2ef292eacf7b46029 Homepage: http://sanger-pathogens.github.io/Roary/ Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-1_all.deb Size: 183740 MD5sum: 991a49663368c3a0a660af3107720dad SHA256: 1732e00b165a0cee53b42fb9b142ea5491cd7de00b91be2cc8709297d999de66 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m3.5s INFO: apt-cache knows about the following packages: roary 0m3.5s INFO: Running scripts pre_install 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy'] 0m3.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy', 'roary'] 0m3.6s DUMP: roary: Installed: (none) Candidate: 3.13.0+dfsg-1 Version table: 3.13.0+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy', 'roary'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-y', 'install', 'roary'] 0m23.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libatomic1 libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libclass-xsaccessor-perl libclone-perl libconst-fast-perl libcurl4t64 libdata-compare-perl libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-chdir-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libpath-tiny-perl libperl5.40 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsharpyuv0 libsm6 libspiffy-perl libsqlite3-0 libssh2-1t64 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3t64 libtk8.6 libtry-tiny-perl liburi-perl libuv1t64 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6t64 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.40 perl-openssl-defaults prank procps python3 python3-minimal python3.12 python3.12-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip Suggested packages: groff-base libxml-sax-expatxs-perl libscalar-properties-perl gdbm-l10n low-memory-monitor krb5-doc krb5-user libdata-dump-perl libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl libdbd-csv-perl liblog-dispatch-filerotate-perl librrds-perl libxml-dom-perl libcrypt-ssleay-perl libscalar-number-perl lm-sensors tcl8.6 tk8.6 libsub-name-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl mcl-doc csh fish ksh tcsh zsh perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl debhelper python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-knitr r-cran-magick r-cran-rmarkdown r-cran-sf r-cran-bit64 r-cran-dbi r-cran-dplyr r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr readline-doc isag Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-sax-perl libxml-sax-writer-perl libxml-libxml-perl libclass-c3-xs-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libdevel-lexalias-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libio-compress-brotli-perl krb5-locales libldap-common libipc-shareable-perl liblog-dispatch-perl libdevel-partialdump-perl libgpm2 libunicode-utf8-perl publicsuffix libsasl2-modules libmodule-pluggable-perl libtext-csv-xs-perl libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl blast2 lynx ruby psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-dbi r-cran-rsqlite r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms r-cran-stringi r-cran-data.table r-cran-mockr r-cran-formattable r-cran-generics r-cran-pkgdown r-cran-zeallot systemd | cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libatomic1 libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libclass-xsaccessor-perl libclone-perl libconst-fast-perl libcurl4t64 libdata-compare-perl libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-chdir-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libpath-tiny-perl libperl5.40 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsharpyuv0 libsm6 libspiffy-perl libsqlite3-0 libssh2-1t64 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3t64 libtk8.6 libtry-tiny-perl liburi-perl libuv1t64 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6t64 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.40 perl-openssl-defaults prank procps python3 python3-minimal python3.12 python3.12-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 240 newly installed, 0 to remove and 0 not upgraded. Need to get 138 MB of archives. After this operation, 415 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:11 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 xz-utils amd64 5.6.3-1+b1 [542 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:40 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libarray-utils-perl all 0.5-3 [6184 B] Get:65 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:66 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.2 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:96 http://deb.debian.org/debian trixie/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:97 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:106 http://deb.debian.org/debian trixie/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:107 http://deb.debian.org/debian trixie/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get:112 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get:114 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1+b1 [99.7 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:128 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libdigest-md5-file-perl all 0.08-1.1 [9608 B] Get:135 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libfile-grep-perl all 0.02-3 [8352 B] Get:140 http://deb.debian.org/debian trixie/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get:141 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libheap-perl all 0.80-5 [34.3 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libset-object-perl amd64 1.42-1+b5 [37.6 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libgraph-perl all 1:0.9729-1 [108 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libparse-yapp-perl all 1.21-4 [41.5 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b3 [198 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libgraph-readwrite-perl all 2.10-1 [45.2 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 liblog-log4perl-perl all 1.57-1 [367 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get:170 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.9 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1+b2 [766 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libpadwalker-perl amd64 2.5-1+b6 [18.6 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:181 http://deb.debian.org/debian trixie/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 libtest-file-perl all 1.993-1 [24.5 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libtest2-suite-perl all 0.000163-1 [383 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libtest-output-perl all 1.034-1 [16.0 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 libtingea0 amd64 21-361-2+b2 [52.1 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 mcl amd64 1:22-282+ds-2 [474 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get:205 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:212 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 roary all 3.13.0+dfsg-1 [184 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 138 MB in 5s (28.6 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5152 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding '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' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding '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' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... 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Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... 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 libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up zip (3.0-14) ... Setting up libblas3:amd64 (3.12.0-4) ... 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+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up xz-utils (5.6.3-1+b1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up procps (2:4.0.4-6) ... Setting up libtingea0:amd64 (21-361-2+b2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b4) ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libset-object-perl (1.42-1+b5) ... Setting up liblog-log4perl-perl (1.57-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up mcl (1:22-282+ds-2) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up libperlio-utf8-strict-perl (0.010-1+b3) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libenv-path-perl (0.19-4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up libfile-grep-perl (0.02-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libfile-chdir-perl (0.1008-1.2) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up liburi-perl (5.30-1) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-2) ... Setting up cd-hit (4.8.1-4) ... Setting up libarray-utils-perl (0.5-3) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-slurper-perl (0.014-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libparse-yapp-perl (1.21-4) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libtest-file-perl (1.993-1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libheap-perl (0.80-5) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libpadwalker-perl (2.5-1+b6) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libexception-class-perl (1.45-1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up libio-all-perl (0.87-2) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libgraph-perl (1:0.9729-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libdata-compare-perl (1.29-1) ... Setting up libio-string-perl (1.08-4) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libtext-diff-perl (1.45-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libtest-output-perl (1.034-1) ... Setting up parallel (20240222+ds-2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up python3.12 (3.12.7-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up libconst-fast-perl (0.014-2) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libtest-most-perl (0.38-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-61-1) ... Setting up python3 (3.12.6-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up r-cran-glue (1.7.0-1) ... Setting up libtest-files-perl (0.26-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up libclass-load-perl (0.25-2) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b4) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up bioperl (1.7.8-1) ... Setting up libmoose-perl:amd64 (2.2207-1+b2) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libdigest-md5-file-perl (0.08-1.1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up libgraph-readwrite-perl (2.10-1) ... Setting up roary (3.13.0+dfsg-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-y', 'install', 'roary'] 0m23.5s INFO: Running scripts post_install 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m24.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m24.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5bzj4fd0 to sid 0m24.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m24.1s INFO: Running scripts pre_distupgrade 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'update'] 0m26.2s 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 [7343 kB] Fetched 17.6 MB in 2s (11.4 MB/s) Reading package lists... 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'update'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-yf', 'dist-upgrade'] 0m28.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt e2fsprogs libapt-pkg6.0t64 libc-bin libc6 libcom-err2 libdebconfclient0 libext2fs2t64 libgpg-error0 libpython3-stdlib libss2 logsave python3 python3-minimal roary 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7158 kB of archives. After this operation, 109 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-4 [2804 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.16 [1113 kB] Get:3 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.16 [1397 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-4 [626 kB] Get:5 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.2~rc1-1 [23.5 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.2~rc1-1 [211 kB] Get:7 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.2~rc1-1 [589 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:11 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.274 [10.1 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.51-2 [82.1 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2~rc1-1 [23.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.2~rc1-1 [28.3 kB] Get:15 http://deb.debian.org/debian sid/main amd64 roary all 3.13.0+dfsg-2 [185 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7158 kB in 0s (31.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19561 files and directories currently installed.) Preparing to unpack .../libc6_2.40-4_amd64.deb ... Unpacking libc6:amd64 (2.40-4) over (2.40-3) ... Setting up libc6:amd64 (2.40-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19561 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.16_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.16) over (2.9.14) ... Setting up libapt-pkg6.0t64:amd64 (2.9.16) ... (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 ... 19561 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.16_amd64.deb ... Unpacking apt (2.9.16) over (2.9.14) ... Setting up apt (2.9.16) ... (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 ... 19561 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-4_amd64.deb ... Unpacking libc-bin (2.40-4) over (2.40-3) ... Setting up libc-bin (2.40-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19561 files and directories currently installed.) Preparing to unpack .../logsave_1.47.2~rc1-1_amd64.deb ... Unpacking logsave (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../libext2fs2t64_1.47.2~rc1-1_amd64.deb ... Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Leaving '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' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Leaving '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' Unpacking libext2fs2t64:amd64 (1.47.2~rc1-1) over (1.47.1-1+b1) ... Setting up libext2fs2t64:amd64 (1.47.2~rc1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19559 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.2~rc1-1_amd64.deb ... Unpacking e2fsprogs (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) over (3.12.6-1) ... Setting up python3-minimal (3.12.7-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19558 files and directories currently installed.) Preparing to unpack .../python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../libdebconfclient0_0.274_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.274) over (0.273) ... Setting up libdebconfclient0:amd64 (0.274) ... (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 ... 19558 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.51-2_amd64.deb ... Unpacking libgpg-error0:amd64 (1.51-2) over (1.50-4) ... Setting up libgpg-error0:amd64 (1.51-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19558 files and directories currently installed.) Preparing to unpack .../libcom-err2_1.47.2~rc1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../libss2_1.47.2~rc1-1_amd64.deb ... Unpacking libss2:amd64 (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../roary_3.13.0+dfsg-2_all.deb ... Unpacking roary (3.13.0+dfsg-2) over (3.13.0+dfsg-1) ... Setting up libcom-err2:amd64 (1.47.2~rc1-1) ... Setting up libss2:amd64 (1.47.2~rc1-1) ... Setting up logsave (1.47.2~rc1-1) ... Setting up roary (3.13.0+dfsg-2) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up e2fsprogs (1.47.2~rc1-1) ... Setting up python3 (3.12.7-1) ... Processing triggers for libc-bin (2.40-4) ... 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-yf', 'dist-upgrade'] 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m29.3s DUMP: 985d16811890b277e37827a9b83e9cc8 - 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m29.5s DUMP: Package: roary Version: 3.13.0+dfsg-2 Installed-Size: 732 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description-en: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. Description-md5: 6d457fd706202fc2ef292eacf7b46029 Homepage: https://sanger-pathogens.github.io/Roary/ Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.13.0+dfsg-2_all.deb Size: 185372 MD5sum: b9a0608203b4c68c800b0b143f644c54 SHA256: d17eb6670706c80adb047f608f299e09cad011f4d21f330036010db9152cd648 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'show', '--no-all-versions', 'roary'] 0m29.5s INFO: apt-cache knows about the following packages: roary 0m29.5s INFO: Running scripts pre_install 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_database-server'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_database-server'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_exceptions'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_exceptions'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_extras'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_extras'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy'] 0m29.5s 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: 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy', 'roary'] 0m29.6s DUMP: roary: Installed: 3.13.0+dfsg-2 Candidate: 3.13.0+dfsg-2 Version table: *** 3.13.0+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy', 'roary'] 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-y', 'install', 'roary'] 0m29.8s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-y', 'install', 'roary'] 0m29.8s INFO: Running scripts post_install 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_install_exceptions'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_install_exceptions'] 0m29.9s INFO: Running scripts post_distupgrade 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_exceptions'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_exceptions'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m29.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m30.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m30.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m31.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m31.1s INFO: Running scripts pre_install 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_database-server'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_database-server'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_exceptions'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_exceptions'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_extras'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_extras'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy'] 0m31.2s 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: 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy', 'roary'] 0m31.2s DUMP: roary: Installed: 3.13.0+dfsg-2 Candidate: 3.13.0+dfsg-2 Version table: *** 3.13.0+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-cache', 'policy', 'roary'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-2'] 0m31.5s DUMP: Reading package lists... Building dependency tree... Reading state information... roary is already the newest version (3.13.0+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', '-y', 'install', 'roary=3.13.0+dfsg-2'] 0m31.5s INFO: Running scripts post_install 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_install_exceptions'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_install_exceptions'] 0m31.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m32.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m32.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', '-ac', '--ignore-obsolete'] 0m34.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', '-ac', '--ignore-obsolete'] 0m34.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m34.1s DUMP: 0.15.6 0m34.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m34.1s INFO: Running adequate version 0.15.6 now. 0m34.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'roary'] 0m34.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'roary'] 0m34.3s INFO: Running scripts pre_remove 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m36.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m36.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_exceptions'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/pre_remove_exceptions'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m36.7s DUMP: install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bioperl bioperl 1.7.8-1 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed coreutils coreutils 9.5-1+b1 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 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-1 install ok installed fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-1.1+b1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 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 gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 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+b1 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.11-2 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.201-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.16 install ok installed libarray-utils-perl libarray-utils-perl 0.5-3 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libb-hooks-op-check-perl:amd64 libb-hooks-op-check-perl 0.22-3+b2 install ok installed libbio-perl-perl libbio-perl-perl 1.7.8-1 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 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 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.48-2 install ok installed libclass-c3-perl libclass-c3-perl 0.35-2 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.10-1 install ok installed libclass-load-perl libclass-load-perl 0.25-2 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.10-2+b4 install ok installed libclass-xsaccessor-perl libclass-xsaccessor-perl 1.19-4+b4 install ok installed libclone-perl:amd64 libclone-perl 0.47-1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-1 install ok installed libconst-fast-perl libconst-fast-perl 0.014-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl4t64:amd64 libcurl4t64 8.11.0-1 install ok installed libdata-compare-perl libdata-compare-perl 1.29-1 install ok installed libdata-optlist-perl libdata-optlist-perl 0.114-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libdevel-callchecker-perl:amd64 libdevel-callchecker-perl 0.009-1+b1 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-4 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.007-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0500-1 install ok installed libdigest-md5-file-perl libdigest-md5-file-perl 0.08-1.1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-2 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.004-1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed libenv-path-perl libenv-path-perl 0.19-4 install ok installed libeval-closure-perl libeval-closure-perl 0.14-3 install ok installed libexception-class-perl libexception-class-perl 1.45-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-chdir-perl libfile-chdir-perl 0.1008-1.2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfile-grep-perl libfile-grep-perl 0.02-3 install ok installed libfile-listing-perl libfile-listing-perl 6.16-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.014-1 install ok installed libfile-which-perl libfile-which-perl 1.27-2 install ok installed libfindbin-libs-perl libfindbin-libs-perl 3.0.2-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 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 14.2.0-8 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 14.2.0-8 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libgraph-perl libgraph-perl 1:0.9729-1 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.10-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libheap-perl libheap-perl 0.80-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.83-1+b1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.24-1 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.11-1 install ok installed libhttp-date-perl libhttp-date-perl 6.06-1 install ok installed libhttp-message-perl libhttp-message-perl 7.00-2 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libio-all-perl libio-all-perl 0.87-2 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.089-1 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 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 3.12.0-4 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.57-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.14-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-3 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-3 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-3 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-2 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-2 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-2 install ok installed libmoose-perl:amd64 libmoose-perl 2.2207-1+b2 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libmro-compat-perl libmro-compat-perl 0.15-2 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnet-http-perl libnet-http-perl 6.23-1 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.94-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.18-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.40-1 install ok installed libpackage-stash-xs-perl:amd64 libpackage-stash-xs-perl 0.30-1+b4 install ok installed libpadwalker-perl libpadwalker-perl 2.5-1+b6 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-3 install ok installed libpaper-utils libpaper-utils 1.1.29+b2 install ok installed libpaper1:amd64 libpaper1 1.1.29+b2 install ok installed libparams-classify-perl:amd64 libparams-classify-perl 0.015-2+b4 install ok installed libparams-util-perl libparams-util-perl 1.102-3+b1 install ok installed libparse-yapp-perl libparse-yapp-perl 1.21-4 install ok installed libpath-tiny-perl libpath-tiny-perl 0.146-1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.010-1+b3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-6 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.7-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 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 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsensors-config libsensors-config 1:3.6.0-10 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-10+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libset-object-perl libset-object-perl 1.42-1+b5 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2~rc1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsub-exporter-perl libsub-exporter-perl 0.990-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-3 install ok installed libsub-install-perl libsub-install-perl 0.929-1 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2800-3 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libtest-deep-perl libtest-deep-perl 1.204-1 install ok installed libtest-differences-perl libtest-differences-perl 0.71-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-3 install ok installed libtest-file-perl libtest-file-perl 1.993-1 install ok installed libtest-files-perl libtest-files-perl 0.26-1 install ok installed libtest-most-perl libtest-most-perl 0.38-1 install ok installed libtest-output-perl libtest-output-perl 1.034-1 install ok installed libtest-warn-perl libtest-warn-perl 0.37-2 install ok installed libtest2-suite-perl libtest2-suite-perl 0.000163-1 install ok installed libtext-csv-perl libtext-csv-perl 2.04-1 install ok installed libtext-diff-perl libtext-diff-perl 1.45-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtingea0:amd64 libtingea0 21-361-2+b2 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+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.32-1 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed liburi-perl liburi-perl 5.30-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-7 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwww-perl libwww-perl 6.77-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b2 install ok installed libxml-parser-perl libxml-parser-perl 2.47-1+b3 install ok installed libxml-writer-perl libxml-writer-perl 0.900-2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b2 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.2~rc1-1 install ok installed mafft mafft 7.505-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mcl mcl 1:22-282+ds-2 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-11 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-6+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-5 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed parallel parallel 20240222+ds-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b2 install ok installed prank prank 0.0.170427+dfsg-3 install ok installed procps procps 2:4.0.4-6 install ok installed python3 python3 3.12.7-1 install ok installed python3-minimal python3-minimal 3.12.7-1 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed r-base-core r-base-core 4.4.2-1 install ok installed r-cran-cli r-cran-cli 3.6.3-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-1+dfsg-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.2-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.5.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gtable r-cran-gtable 0.3.6+dfsg-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-61-1 install ok installed r-cran-matrix r-cran-matrix 1.7-1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-munsell r-cran-munsell 0.5.1-1 install ok installed r-cran-nlme r-cran-nlme 3.1.166-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-withr r-cran-withr 3.0.2+dfsg-1 install ok installed readline-common readline-common 8.2-5 install ok installed roary roary 3.13.0+dfsg-2 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sysstat sysstat 12.7.5-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.2.1-2 install ok installed xz-utils xz-utils 5.6.3-1+b1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'remove', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libatomic1:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-xsaccessor-perl', 'libclone-perl:amd64', 'libconst-fast-perl', 'libcurl4t64:amd64', 'libdata-compare-perl', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-chdir-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpath-tiny-perl', 'libperl5.40:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libsub-uplevel-perl', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-warn-perl', 'libtest2-suite-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.12', 'python3.12-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip', 'roary'] 0m38.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bedtools bioperl ca-certificates cd-hit fasttree fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libalgorithm-c3-perl libalgorithm-diff-perl libarray-utils-perl libatomic1 libb-hooks-op-check-perl libbio-perl-perl libblas3 libbrotli1 libcairo2 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libclass-xsaccessor-perl libclone-perl libconst-fast-perl libcurl4t64 libdata-compare-perl libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl libdist-checkconflicts-perl libdynaloader-functions-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libfile-chdir-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblmdb0 liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl2 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparse-yapp-perl libpath-tiny-perl libperl5.40 libperlio-utf8-strict-perl libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-object-perl libsharpyuv0 libsm6 libspiffy-perl libsqlite3-0 libssh2-1t64 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libsub-uplevel-perl libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libthai-data libthai0 libtiff6 libtimedate-perl libtingea0 libtirpc-common libtirpc3t64 libtk8.6 libtry-tiny-perl liburi-perl libuv1t64 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxrender1 libxss1 libxt6t64 mafft mcl media-types ncbi-blast+ ncbi-data netbase openssl parallel perl perl-modules-5.40 perl-openssl-defaults prank procps python3 python3-minimal python3.12 python3.12-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common roary sensible-utils sysstat ucf unzip x11-common xdg-utils xz-utils zip 0 upgraded, 0 newly installed, 240 to remove and 0 not upgraded. After this operation, 415 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 ... 19566 files and directories currently installed.) Removing roary (3.13.0+dfsg-2) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bioperl (1.7.8-1) ... Removing r-cran-ggplot2 (3.5.1+dfsg-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-withr (3.0.2+dfsg-1) ... Removing libgraph-readwrite-perl (2.10-1) ... Removing libxml-parser-perl (2.47-1+b3) ... Removing cd-hit (4.8.1-4) ... Removing fasttree (2.1.11-2) ... Removing libmoose-perl:amd64 (2.2207-1+b2) ... Removing libdevel-overloadinfo-perl (0.007-1) ... Removing libmro-compat-perl (0.15-2) ... Removing libclass-c3-perl (0.35-2) ... Removing libalgorithm-c3-perl (0.11-2) ... Removing libtest-files-perl (0.26-1) ... Removing libtest-most-perl (0.38-1) ... Removing libtest-differences-perl (0.71-1) ... Removing libtext-diff-perl (1.45-2) ... Removing libalgorithm-diff-perl (1.201-1) ... Removing libarray-utils-perl (0.5-3) ... Removing libmodule-runtime-conflicts-perl (0.003-2) ... Removing libpackage-deprecationmanager-perl (0.18-1) ... Removing libbio-perl-perl (1.7.8-1) ... Removing libtest-output-perl (1.034-1) ... Removing libcapture-tiny-perl (0.48-2) ... Removing libexception-class-perl (1.45-1) ... Removing libclass-data-inheritable-perl (0.10-1) ... Removing libclass-load-xs-perl (0.10-2+b4) ... Removing libclass-load-perl (0.25-2) ... Removing libclass-xsaccessor-perl (1.19-4+b4) ... Removing libdata-compare-perl (1.29-1) ... Removing libconst-fast-perl (0.014-2) ... Removing libeval-closure-perl (0.14-3) ... Removing libsub-exporter-perl (0.990-1) ... Removing libdata-optlist-perl (0.114-1) ... Removing libdata-stag-perl (0.14-3) ... Removing libdevel-globaldestruction-perl (0.14-4) ... Removing libdevel-stacktrace-perl (2.0500-1) ... Removing libdigest-md5-file-perl (0.08-1.1) ... Removing libdist-checkconflicts-perl (0.11-2) ... Removing libenv-path-perl (0.19-4) ... Removing ncbi-blast+ (2.16.0+ds-6+b1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libfile-chdir-perl (0.1008-1.2) ... Removing libfile-find-rule-perl (0.34-3) ... Removing libfile-grep-perl (0.02-3) ... Removing libfile-slurper-perl (0.014-1) ... Removing libfile-which-perl (1.27-2) ... Removing libfindbin-libs-perl (3.0.2-1) ... Removing parallel (20240222+ds-2) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing libtest2-suite-perl (0.000163-1) ... Removing libio-all-perl (0.87-2) ... Removing libspiffy-perl (0.46-1) ... Removing mafft (7.505-1) ... Removing libtest-deep-perl (1.204-1) ... Removing libgraph-perl (1:0.9729-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libheap-perl (0.80-5) ... Removing libio-string-perl (1.08-4) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing liblog-log4perl-perl (1.57-1) ... Removing libmbedtls21:amd64 (3.6.2-3) ... Removing libmbedx509-7:amd64 (3.6.2-3) ... Removing libmbedcrypto16:amd64 (3.6.2-3) ... Removing procps (2:4.0.4-6) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libnumber-compare-perl (0.03-3) ... Removing libpackage-stash-xs-perl:amd64 (0.30-1+b4) ... Removing libpadwalker-perl (2.5-1+b6) ... Removing libparams-util-perl (1.102-3+b1) ... Removing libparse-yapp-perl (1.21-4) ... Removing libpath-tiny-perl (0.146-1) ... Removing libperlio-utf8-strict-perl (0.010-1+b3) ... Removing libproc2-0:amd64 (2:4.0.4-6) ... Removing libpython3.12-minimal:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing sysstat (12.7.5-2) ... Removing libsensors5:amd64 (1:3.6.0-10+b1) ... Removing libsensors-config (1:3.6.0-10) ... Removing libset-object-perl (1.42-1+b5) ... Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libsub-exporter-progressive-perl (0.001013-3) ... Removing libsub-install-perl (0.929-1) ... Removing libtest-warn-perl (0.37-2) ... Removing libtest-exception-perl (0.43-3) ... Removing libsub-uplevel-perl (0.2800-3) ... Removing libtest-file-perl (1.993-1) ... Removing libtext-csv-perl (2.04-1) ... Removing libtext-glob-perl (0.11-3) ... Removing mcl (1:22-282+ds-2) ... Removing libtingea0:amd64 (21-361-2+b2) ... Removing libuv1t64:amd64 (1.48.0-7) ... Removing libxml-writer-perl (0.900-2) ... Removing media-types (10.1.0) ... Removing ncbi-data (6.1.20170106+dfsg2-5) ... Removing prank (0.0.170427+dfsg-3) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-gtable (0.3.6+dfsg-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-cli (3.6.3-1) ... Removing r-cran-munsell (0.5.1-1) ... Removing r-cran-colorspace (2.1-1+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.2-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.166-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-61-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing xz-utils (5.6.3-1+b1) ... Removing r-base-core (4.4.2-1) ... Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-3) ... Removing fontconfig (2.15.0-1.1+b1) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b2) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing libpackage-stash-perl (0.40-1) ... Removing libmodule-implementation-perl (0.09-2) ... Removing libmodule-runtime-perl (0.016-2) ... Removing libparams-classify-perl:amd64 (0.015-2+b4) ... Removing libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Removing libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.11.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libdynaloader-functions-perl (0.004-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... 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 libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Removing libsm6:amd64 (2:1.2.4-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpaper-utils (1.1.29+b2) ... Removing libpaper1:amd64 (1.1.29+b2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing readline-common (8.2-5) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... 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 xdg-utils (1.2.1-2) ... Removing zip (3.0-14) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing libwww-perl (6.77-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libfile-listing-perl (6.16-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libhttp-cookies-perl (6.11-1) ... Removing liblwp-protocol-https-perl (6.14-1) ... Removing libnet-http-perl (6.23-1) ... Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.83-1+b1) ... Removing libhtml-tagset-perl (3.24-1) ... Removing libio-socket-ssl-perl (2.089-1) ... Removing libnet-ssleay-perl:amd64 (1.94-2) ... Removing libtry-tiny-perl (0.32-1) ... Removing netbase (6.4) ... Removing perl-openssl-defaults:amd64 (7+b2) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (7.00-2) ... Removing libclone-perl:amd64 (0.47-1+b1) ... Removing libencode-locale-perl (1.05-3) ... Removing libhttp-date-perl (6.06-1) ... Removing liburi-perl (5.30-1) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing libtimedate-perl (2.3300-2) ... Removing openssl (3.3.2-2) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing perl-modules-5.40 (5.40.0-8) ... Processing triggers for libc-bin (2.40-4) ... 0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'remove', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libatomic1:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-xsaccessor-perl', 'libclone-perl:amd64', 'libconst-fast-perl', 'libcurl4t64:amd64', 'libdata-compare-perl', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-chdir-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpath-tiny-perl', 'libperl5.40:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libsub-uplevel-perl', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-warn-perl', 'libtest2-suite-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.12', 'python3.12-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip', 'roary'] 0m38.5s INFO: Running scripts post_remove 0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_remove_exceptions'] 0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_remove_exceptions'] 0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--purge', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libatomic1:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-xsaccessor-perl', 'libclone-perl:amd64', 'libconst-fast-perl', 'libcurl4t64:amd64', 'libdata-compare-perl', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-chdir-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpath-tiny-perl', 'libperl5.40:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libsub-uplevel-perl', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-warn-perl', 'libtest2-suite-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.12', 'python3.12-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 0m39.1s DUMP: dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bioperl which isn't installed (Reading database ... 5220 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed Purging configuration files for fontconfig (2.15.0-1.1+b1) ... Purging configuration files for fontconfig-config (2.15.0-1.1+b1) ... 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 dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-perl which isn't installed dpkg: warning: ignoring request to remove libarray-utils-perl which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libb-hooks-op-check-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl 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 libcapture-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libclass-c3-perl which isn't installed dpkg: warning: ignoring request to remove libclass-data-inheritable-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-xs-perl which isn't installed dpkg: warning: ignoring request to remove libclass-xsaccessor-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libconst-fast-perl which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdata-compare-perl which isn't installed dpkg: warning: ignoring request to remove libdata-optlist-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdevel-callchecker-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-globaldestruction-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-overloadinfo-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-stacktrace-perl which isn't installed dpkg: warning: ignoring request to remove libdigest-md5-file-perl which isn't installed dpkg: warning: ignoring request to remove libdist-checkconflicts-perl which isn't installed dpkg: warning: ignoring request to remove libdynaloader-functions-perl which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libenv-path-perl which isn't installed dpkg: warning: ignoring request to remove libeval-closure-perl which isn't installed dpkg: warning: ignoring request to remove libexception-class-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-chdir-perl which isn't installed dpkg: warning: ignoring request to remove libfile-find-rule-perl which isn't installed dpkg: warning: ignoring request to remove libfile-grep-perl which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfile-slurper-perl which isn't installed dpkg: warning: ignoring request to remove libfile-which-perl which isn't installed dpkg: warning: ignoring request to remove libfindbin-libs-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 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 (2.82.2-3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraph-perl which isn't installed dpkg: warning: ignoring request to remove libgraph-readwrite-perl 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 libheap-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl 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 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 liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblog-log4perl-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-conflicts-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmoose-perl which isn't installed dpkg: warning: ignoring request to remove libmro-compat-perl which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libnumber-compare-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-deprecationmanager-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-xs-perl which isn't installed dpkg: warning: ignoring request to remove libpadwalker-perl which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29+b2) ... dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libparse-yapp-perl which isn't installed dpkg: warning: ignoring request to remove libpath-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libperlio-utf8-strict-perl 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 libproc2-0 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 (3.12.7-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib 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 Purging configuration files for libsensors-config (1:3.6.0-10) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libset-object-perl which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libspiffy-perl 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 libsub-exporter-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libsub-install-perl which isn't installed dpkg: warning: ignoring request to remove libsub-uplevel-perl which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtest-deep-perl which isn't installed dpkg: warning: ignoring request to remove libtest-differences-perl which isn't installed dpkg: warning: ignoring request to remove libtest-exception-perl which isn't installed dpkg: warning: ignoring request to remove libtest-file-perl which isn't installed dpkg: warning: ignoring request to remove libtest-files-perl which isn't installed dpkg: warning: ignoring request to remove libtest-most-perl which isn't installed dpkg: warning: ignoring request to remove libtest-output-perl which isn't installed dpkg: warning: ignoring request to remove libtest-warn-perl which isn't installed dpkg: warning: ignoring request to remove libtest2-suite-perl which isn't installed dpkg: warning: ignoring request to remove libtext-csv-perl which isn't installed dpkg: warning: ignoring request to remove libtext-diff-perl which isn't installed dpkg: warning: ignoring request to remove libtext-glob-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtingea0 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+b1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl 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 libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-writer-perl which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove mcl which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-5) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for parallel (20240222+ds-2) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed Purging configuration files for procps (2:4.0.4-6) ... Purging configuration files for python3 (3.12.7-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... Purging configuration files for r-base-core (4.4.2-1) ... dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-colorspace which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-farver which isn't installed dpkg: warning: ignoring request to remove r-cran-ggplot2 which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-isoband which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-mgcv which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rcolorbrewer which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sysstat (12.7.5-2) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--purge', 'bedtools', 'bioperl', 'ca-certificates', 'cd-hit', 'fasttree', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libarray-utils-perl', 'libatomic1:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-xsaccessor-perl', 'libclone-perl:amd64', 'libconst-fast-perl', 'libcurl4t64:amd64', 'libdata-compare-perl', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdigest-md5-file-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libencode-locale-perl', 'libenv-path-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfile-chdir-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libheap-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-html-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblog-log4perl-perl', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnumber-compare-perl', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libparse-yapp-perl', 'libpath-tiny-perl', 'libperl5.40:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-object-perl', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libsub-uplevel-perl', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-warn-perl', 'libtest2-suite-perl', 'libtext-csv-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtingea0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml-parser-perl', 'libxml-writer-perl', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'mafft', 'mcl', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'prank', 'procps', 'python3', 'python3-minimal', 'python3.12', 'python3.12-minimal', 'r-base-core', 'r-cran-cli', 'r-cran-colorspace', 'r-cran-fansi', 'r-cran-farver', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-isoband', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rlang', 'r-cran-scales', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'sensible-utils', 'sysstat', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xz-utils', 'zip'] 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--purge', 'roary'] 0m39.1s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--purge', 'roary'] 0m39.1s INFO: Running scripts post_purge 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_purge_exceptions'] 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_purge_exceptions'] 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--purge', '--pending'] 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--purge', '--pending'] 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--remove', '--pending'] 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg', '--remove', '--pending'] 0m39.1s INFO: Running scripts post_test 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_test_exceptions'] 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'tmp/scripts/post_test_exceptions'] 0m39.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m39.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg-divert', '--list'] 0m39.3s 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 0m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'dpkg-divert', '--list'] 0m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'clean'] 0m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0', 'apt-get', 'clean'] 0m39.4s DEBUG: Recording chroot state 0m39.7s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, 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 0m39.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/shm'] 0m39.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/shm'] 0m39.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/console'] 0m39.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/console'] 0m39.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/ptmx'] 0m39.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/ptmx'] 0m39.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/pts'] 0m39.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/dev/pts'] 0m39.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/proc'] 0m39.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0/proc'] 0m39.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m40.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5bzj4fd0'] 0m40.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5bzj4fd0 0m40.0s INFO: PASS: Upgrading between Debian distributions. 0m40.0s INFO: PASS: All tests. 0m40.0s INFO: piuparts run ends. ret=0 End: 2024-12-02 21:20:46 GMT