Start: 2024-11-07 15:28:37 GMT [testing] Package: qcumber Version: 2.3.0-2 Installed-Size: 236 Maintainer: Debian Med Packaging Team Architecture: all Replaces: qc-pipeline Provides: qc-pipeline Depends: python3:any, debconf (>= 0.5) | debconf-2.0, python3-jinja2, python3-matplotlib, python3-biopython, libjs-angularjs, libjs-bootstrap, libjs-d3, libjs-jquery, r-base-core, r-bioc-savr, r-cran-ggplot2, r-cran-quantreg, snakemake Conflicts: qc-pipeline Description: quality control of genomic sequences Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber Description-md5: 380ba80499911de0a248a18cb1009872 Section: science Priority: optional Filename: pool/main/q/qcumber/qcumber_2.3.0-2_all.deb Size: 50488 MD5sum: e8e75d1efdd4265bdbe9e121b7109314 SHA256: 033afeb7358c5e35109c648bbc275842755dc14c328f84007af5a389c06501cb [sid] Package: qcumber Version: 2.3.0-2 Installed-Size: 236 Maintainer: Debian Med Packaging Team Architecture: all Replaces: qc-pipeline Provides: qc-pipeline Depends: python3:any, debconf (>= 0.5) | debconf-2.0, python3-jinja2, python3-matplotlib, python3-biopython, libjs-angularjs, libjs-bootstrap, libjs-d3, libjs-jquery, r-base-core, r-bioc-savr, r-cran-ggplot2, r-cran-quantreg, snakemake Conflicts: qc-pipeline Description: quality control of genomic sequences Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber Description-md5: 380ba80499911de0a248a18cb1009872 Section: science Priority: optional Filename: pool/main/q/qcumber/qcumber_2.3.0-2_all.deb Size: 50488 MD5sum: e8e75d1efdd4265bdbe9e121b7109314 SHA256: 033afeb7358c5e35109c648bbc275842755dc14c328f84007af5a389c06501cb 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 qcumber=2.3.0-2 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 qcumber=2.3.0-2 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/tmprwr7rloc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmprwr7rloc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', '--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/tmprwr7rloc', '--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/tmprwr7rloc/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/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/tmprwr7rloc/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/tmprwr7rloc/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmprwr7rloc/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'update'] 0m1.6s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9341 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6241 kB] Fetched 15.8 MB in 1s (17.2 MB/s) Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: coreutils libssl3t64 libsystemd0 libudev1 openssl-provider-legacy 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6019 kB of archives. After this operation, 296 kB disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.3.2-2 [298 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.3.2-2 [2271 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 256.7-3 [382 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 256.7-3 [145 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6019 kB in 0s (55.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5166 files and directories currently installed.) Preparing to unpack .../coreutils_9.5-1+b1_amd64.deb ... Unpacking coreutils (9.5-1+b1) over (9.4-3.1) ... Setting up coreutils (9.5-1+b1) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.3.2-2_amd64.deb ... Unpacking openssl-provider-legacy (3.3.2-2) over (3.3.2-1) ... Setting up openssl-provider-legacy (3.3.2-2) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.3.2-2_amd64.deb ... Unpacking libssl3t64:amd64 (3.3.2-2) over (3.3.2-1) ... Setting up libssl3t64:amd64 (3.3.2-2) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libsystemd0_256.7-3_amd64.deb ... Unpacking libsystemd0:amd64 (256.7-3) over (256.7-2) ... Setting up libsystemd0:amd64 (256.7-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5167 files and directories currently installed.) Preparing to unpack .../libudev1_256.7-3_amd64.deb ... Unpacking libudev1:amd64 (256.7-3) over (256.7-2) ... Setting up libudev1:amd64 (256.7-3) ... Processing triggers for libc-bin (2.40-3) ... 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 656961bed45e71a26979cb287e562a45 - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s 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' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 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 1:2.40.2-9 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 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-6 install ok installed gpgv gpgv 2.2.44-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 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 0.272+b1 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 14.2.0-6 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 3.8.6-2+b1 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 2.40.2-9 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 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 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 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 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+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 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 2.40.2-9 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 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 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 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'show', '--no-all-versions', 'qcumber'] 0m3.7s DUMP: Package: qcumber Version: 2.3.0-2 Installed-Size: 236 Maintainer: Debian Med Packaging Team Architecture: all Replaces: qc-pipeline Provides: qc-pipeline Depends: python3:any, debconf (>= 0.5) | debconf-2.0, python3-jinja2, python3-matplotlib, python3-biopython, libjs-angularjs, libjs-bootstrap, libjs-d3, libjs-jquery, r-base-core, r-bioc-savr, r-cran-ggplot2, r-cran-quantreg, snakemake Conflicts: qc-pipeline Description-en: quality control of genomic sequences QCPipeline is a tool for quality control. The workflow is as follows: . 1. Quality control with FastQC 2. Trim Reads with Trimmomatic 3. Quality control of trimmed reads with FastQC 4. Map reads against reference using bowtie2 5. Classify reads with Kraken Description-md5: 380ba80499911de0a248a18cb1009872 Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber Section: science Priority: optional Filename: pool/main/q/qcumber/qcumber_2.3.0-2_all.deb Size: 50488 MD5sum: e8e75d1efdd4265bdbe9e121b7109314 SHA256: 033afeb7358c5e35109c648bbc275842755dc14c328f84007af5a389c06501cb 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'show', '--no-all-versions', 'qcumber'] 0m3.7s INFO: apt-cache knows about the following packages: qcumber 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy'] 0m3.7s 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: 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy', 'qcumber'] 0m3.7s DUMP: qcumber: Installed: (none) Candidate: 2.3.0-2 Version table: 2.3.0-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy', 'qcumber'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-y', 'install', 'qcumber'] 0m58.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt ca-certificates coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-lyx fonts-urw-base35 git git-man libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 liberror-perl libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-angularjs libjs-bootstrap libjs-d3 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-0-2 littler media-types netbase openssl perl perl-modules-5.40 python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-configargparse python3-connection-pool python3-contourpy python3-cycler python3-dateutil python3-datrie python3-decorator python3-docutils python3-dpath python3-fastjsonschema python3-fonttools python3-freetype python3-fs python3-git python3-gitdb python3-humanfriendly python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbformat python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-plac python3-platformdirs python3-psutil python3-pulp python3-py python3-pyparsing python3-ratelimiter python3-referencing python3-reportlab python3-requests python3-retry python3-rlpycairo python3-roman python3-rpds-py python3-scipy python3-six python3-smart-open python3-smmap python3-stopit python3-sympy python3-tabulate python3-throttler python3-tk python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wrapt python3-yaml python3-yte python3.12 python3.12-minimal python3.12-tk python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-savr r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cpp11 r-cran-data.table r-cran-diagram r-cran-digest r-cran-dplyr r-cran-e1071 r-cran-fansi r-cran-farver r-cran-foreach r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gridextra r-cran-gtable r-cran-hardhat r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-mgcv r-cran-modelmetrics r-cran-munsell r-cran-nlme r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-recipes r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-scales r-cran-shape r-cran-sparsem r-cran-squarem r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xml readline-common sensible-utils sgml-base snakemake tk8.6-blt2.5 ucf unicode-data unzip w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip Suggested packages: blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn gdbm-l10n low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python-charset-normalizer-doc python-cycler-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-fastjsonschema-doc python-git-doc python-jinja2-doc python-jsonschema-doc python3-pip python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools subversion python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python3-azure python3-azure-storage texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python-traitlets-doc python3.12-venv python3.12-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit r-cran-cairo r-cran-testthat r-cran-bradleyterry2 r-cran-covr r-cran-ellipse r-cran-gam r-cran-knitr r-cran-mlbench r-cran-party r-cran-pls r-cran-randomforest r-cran-rann r-cran-rmarkdown r-cran-tinytest r-cran-magick r-cran-sf r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-inline 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 readline-doc sgml-base-doc slurm-client snakemake-doc debhelper Recommended packages: patch less ssh-client libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python-biopython-doc ncbi-blast+ python3-pygments python3-babel python3-json-pointer python3-rfc3987 python3-uritemplate python3-webcolors python3-bs4 python3-cssselect python3-html5lib python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-boto3 python3-paramiko python3-zstandard isympy-common r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-earth r-cran-mda r-cran-mlmetrics r-cran-fastica r-cran-kernlab r-cran-themis r-cran-callr r-cran-covr r-cran-crayon 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-whoami r-cran-slider r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-png r-cran-jpeg r-cran-viridis r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-progress r-cran-bit64 r-cran-bit r-cran-r.utils r-cran-xts r-cran-zoo r-cran-yaml r-cran-markdown r-cran-broom r-cran-dbi r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-unitizer r-cran-rhpcblasctl r-cran-r.rsp r-cran-pkgload r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-ragg r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-waldo r-cran-devtools r-cran-modeldata r-cran-roxygen2 r-cran-usethis r-cran-mlbench r-cran-th.data r-cran-randomforest r-cran-party r-cran-ellipse r-cran-fields r-cran-geepack r-bioc-graph r-cran-bookdown r-cran-igraph r-cran-lavasearch2 r-cran-lme4 r-cran-mets r-cran-optimx r-cran-polycor r-cran-rgl r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-microbenchmark r-cran-r.devices r-cran-abind r-cran-doparallel r-cran-itertools r-cran-logcondens r-cran-pbmcapply r-cran-furrr r-cran-commonmark r-cran-cba r-cran-httr r-cran-ddalpha r-cran-dials r-cran-rann r-cran-rcpproll r-cran-rsample r-cran-rspectra r-cran-splines2 r-cran-rcppml r-cran-dimred r-cran-fs r-cran-dichromat r-cran-hms r-cran-setrng r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot cwltool imagemagick python3-yappi python3-azure-storage python3-botocore python3-dropbox python3-flask python3-ftputil python3-irodsclient python3-kubernetes libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: blt ca-certificates coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-lyx fonts-urw-base35 git git-man libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 liberror-perl libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-angularjs libjs-bootstrap libjs-d3 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-0-2 littler media-types netbase openssl perl perl-modules-5.40 python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-configargparse python3-connection-pool python3-contourpy python3-cycler python3-dateutil python3-datrie python3-decorator python3-docutils python3-dpath python3-fastjsonschema python3-fonttools python3-freetype python3-fs python3-git python3-gitdb python3-humanfriendly python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbformat python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-plac python3-platformdirs python3-psutil python3-pulp python3-py python3-pyparsing python3-ratelimiter python3-referencing python3-reportlab python3-requests python3-retry python3-rlpycairo python3-roman python3-rpds-py python3-scipy python3-six python3-smart-open python3-smmap python3-stopit python3-sympy python3-tabulate python3-throttler python3-tk python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wrapt python3-yaml python3-yte python3.12 python3.12-minimal python3.12-tk python3.13-tk qcumber r-base-core r-bioc-biocgenerics r-bioc-savr r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cpp11 r-cran-data.table r-cran-diagram r-cran-digest r-cran-dplyr r-cran-e1071 r-cran-fansi r-cran-farver r-cran-foreach r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gridextra r-cran-gtable r-cran-hardhat r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-mgcv r-cran-modelmetrics r-cran-munsell r-cran-nlme r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-recipes r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-scales r-cran-shape r-cran-sparsem r-cran-squarem r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xml readline-common sensible-utils sgml-base snakemake tk8.6-blt2.5 ucf unicode-data unzip w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 0 upgraded, 310 newly installed, 0 to remove and 0 not upgraded. Need to get 234 MB of archives. After this operation, 700 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-6 [3022 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-6 [4326 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-6 [267 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:16 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:27 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:44 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b2 [804 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:58 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-6 [836 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-1+b1 [459 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-1+b1 [293 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 liberror-perl all 0.17029-2 [29.0 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 git-man all 1:2.45.2-1 [2158 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 git amd64 1:2.45.2-1 [8645 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-6 [9284 B] Get:87 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-2 [352 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-6 [137 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libjs-angularjs all 1.8.3-1 [817 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:120 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get:136 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-1 [16.0 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:147 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.6-1 [112 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.0-1 [103 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.6-1 [9428 B] Get:154 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1 [79.4 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2 [114 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:159 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.84+dfsg-4 [1646 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b5 [318 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:164 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1 [118 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 python3-configargparse all 1.7-1 [31.3 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get:167 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.0-2 [215 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:169 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 python3-datrie amd64 0.8.2-5 [124 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1 [1251 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b4 [25.2 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-5 [16.7 MB] Get:182 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b2 [298 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.54.1-4 [1429 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 python3-gitdb all 4.0.11-1 [45.5 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 python3-git all 3.1.37-3 [137 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 python3-rpds-py amd64 0.20.1-1 [252 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 python3-referencing all 0.35.1-1 [23.5 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get:198 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2 [60.9 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3 [5560 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 python3-plac all 1.4.3-1 [65.6 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 python3-py all 1.11.0-2 [88.7 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get:212 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 python3-retry all 0.9.2-3 [7088 B] Get:215 http://deb.debian.org/debian trixie/main amd64 python3-wrapt amd64 1.15.0-3 [43.3 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 python3-smart-open all 7.0.4-2 [83.3 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get:220 http://deb.debian.org/debian trixie/main amd64 python3-toposort all 1.10-2 [7336 B] Get:221 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1 [134 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB] Get:254 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:255 http://deb.debian.org/debian trixie/main amd64 r-cran-stringi amd64 1.8.4-1 [895 kB] Get:256 http://deb.debian.org/debian trixie/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get:258 http://deb.debian.org/debian trixie/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 r-bioc-savr all 1.37.0-4 [631 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 r-cran-sparsem amd64 1.84-2-1+b1 [794 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixmodels all 0.5-3-1 [364 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.7-0-1 [6305 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:265 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpparmadillo amd64 14.0.2-1-1 [863 kB] Get:266 http://deb.debian.org/debian trixie/main amd64 r-cran-class amd64 7.3-22-2 [87.3 kB] Get:267 http://deb.debian.org/debian trixie/main amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 r-cran-e1071 amd64 1.7-16-1 [562 kB] Get:269 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:270 http://deb.debian.org/debian trixie/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:271 http://deb.debian.org/debian trixie/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:272 http://deb.debian.org/debian trixie/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get:273 http://deb.debian.org/debian trixie/main amd64 r-cran-modelmetrics amd64 1.2.2.2-1+b1 [125 kB] Get:274 http://deb.debian.org/debian trixie/main amd64 r-cran-proc amd64 1.18.5-1 [987 kB] Get:275 http://deb.debian.org/debian trixie/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:276 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:277 http://deb.debian.org/debian trixie/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:278 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:279 http://deb.debian.org/debian trixie/main amd64 r-cran-tzdb amd64 0.4.0-2 [499 kB] Get:280 http://deb.debian.org/debian trixie/main amd64 r-cran-clock amd64 0.7.1-1 [1784 kB] Get:281 http://deb.debian.org/debian trixie/main amd64 r-cran-gower amd64 1.0.1-1 [207 kB] Get:282 http://deb.debian.org/debian trixie/main amd64 r-cran-hardhat all 1.4.0+dfsg-1 [668 kB] Get:283 http://deb.debian.org/debian trixie/main amd64 r-cran-rpart amd64 4.1.23-1 [685 kB] Get:284 http://deb.debian.org/debian trixie/main amd64 r-cran-nnet amd64 7.3-19-2 [111 kB] Get:285 http://deb.debian.org/debian trixie/main amd64 r-cran-shape all 1.4.6.1-1 [752 kB] Get:286 http://deb.debian.org/debian trixie/main amd64 r-cran-diagram all 1.6.5-2 [656 kB] Get:287 http://deb.debian.org/debian trixie/main amd64 r-cran-kernsmooth amd64 2.23-24-1 [92.7 kB] Get:288 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:289 http://deb.debian.org/debian trixie/main amd64 r-cran-globals all 0.16.3-1 [120 kB] Get:290 http://deb.debian.org/debian trixie/main amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] Get:291 http://deb.debian.org/debian trixie/main amd64 r-cran-parallelly amd64 1.38.0-1 [388 kB] Get:292 http://deb.debian.org/debian trixie/main amd64 r-cran-future all 1.34.0+dfsg-1 [649 kB] Get:293 http://deb.debian.org/debian trixie/main amd64 r-cran-future.apply all 1.11.2+dfsg-1 [172 kB] Get:294 http://deb.debian.org/debian trixie/main amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] Get:295 http://deb.debian.org/debian trixie/main amd64 r-cran-progressr all 0.14.0-1 [337 kB] Get:296 http://deb.debian.org/debian trixie/main amd64 r-cran-squarem all 2021.1-1 [179 kB] Get:297 http://deb.debian.org/debian trixie/main amd64 r-cran-lava all 1.7.3+dfsg-1 [2207 kB] Get:298 http://deb.debian.org/debian trixie/main amd64 r-cran-prodlim amd64 2024.06.25-1 [416 kB] Get:299 http://deb.debian.org/debian trixie/main amd64 r-cran-ipred amd64 0.9-15-1 [387 kB] Get:300 http://deb.debian.org/debian trixie/main amd64 r-cran-timechange amd64 0.3.0-1 [173 kB] Get:301 http://deb.debian.org/debian trixie/main amd64 r-cran-lubridate amd64 1.9.3+dfsg-1 [1018 kB] Get:302 http://deb.debian.org/debian trixie/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:303 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:304 http://deb.debian.org/debian trixie/main amd64 r-cran-timedate amd64 4041.110-1 [1211 kB] Get:305 http://deb.debian.org/debian trixie/main amd64 r-cran-recipes all 1.1.0+dfsg-1 [2047 kB] Get:306 http://deb.debian.org/debian trixie/main amd64 r-cran-caret amd64 6.0-94+dfsg-1 [3446 kB] Get:307 http://deb.debian.org/debian trixie/main amd64 r-cran-conquer amd64 1.3.3-1 [471 kB] Get:308 http://deb.debian.org/debian trixie/main amd64 r-cran-quantreg amd64 5.99-1 [1544 kB] Get:309 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-6 [318 kB] Get:310 http://deb.debian.org/debian trixie/main amd64 qcumber all 2.3.0-2 [50.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 234 MB in 1s (213 MB/s) Selecting previously unselected package perl-modules-5.40. (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 ... 5171 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.40_5.40.0-6_all.deb ... Unpacking perl-modules-5.40 (5.40.0-6) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../2-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../3-libperl5.40_5.40.0-6_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.0-6) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.40.0-6_amd64.deb ... Unpacking perl (5.40.0-6) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../5-libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.6.3-2_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../7-python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-2) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7655 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding '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' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... 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 ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8213 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 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 liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libcurl4t64:amd64 (8.10.1-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up python3.12-tk (3.12.6-1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.0-1) ... Setting up liberror-perl (0.17029-2) ... Setting up coinor-libclp1:amd64 (1.17.10+ds-1) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up git (1:2.45.2-1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up coinor-libcgl1:amd64 (0.60.9+ds-1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.6-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-squarem (2021.1-1) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... 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 r-cran-xml (3.99-0.17-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-sparsem (1.84-2-1+b1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up r-cran-proxy (0.4-27-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-numderiv (2016.8-1.1-3) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-rcpp (1.0.13-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-matrixstats (1.4.1-1) ... Setting up r-cran-listenv (0.9.1+dfsg-1) ... Setting up littler (0.3.20-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-digest (0.6.37-1) ... Setting up r-cran-gower (1.0.1-1) ... Setting up r-cran-timedate (4041.110-1) ... Setting up r-cran-foreach (1.5.2-1) ... 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 python3-freetype (2.5.1-1) ... Setting up r-cran-data.table (1.16.2+dfsg-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up r-cran-glue (1.7.0-1) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up python3-plac (1.4.3-1) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-tz (2024.1-2) ... Setting up r-cran-progressr (0.14.0-1) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up r-cran-shape (1.4.6.1-1) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:amd64 (10.4.0-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up python3-packaging (24.1-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up r-cran-parallelly (1.38.0-1) ... Setting up coinor-cbc (2.10.12+ds-1) ... Setting up r-cran-stringi (1.8.4-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up python3-brotli (1.1.0-2+b5) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-diagram (1.6.5-2) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-dpath (2.2.0-1) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-kiwisolver (1.4.7-2) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-wrapt (1.15.0-3) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up r-cran-kernsmooth (2.23-24-1) ... Setting up python3-rpds-py (0.20.1-1) ... Setting up python3-fastjsonschema (2.20.0-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up python3-lxml:amd64 (5.3.0-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up r-cran-rcpparmadillo (14.0.2-1-1) ... Setting up python3-datrie:amd64 (0.8.2-5) ... Setting up r-cran-tzdb (0.4.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up r-cran-globals (0.16.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-smmap (6.0.0-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up python3-jupyter-core (5.7.2-4) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-toposort (1.10-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-configargparse (1.7-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-cairo (1.26.1-2) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up r-cran-class (7.3-22-2) ... Setting up python3-smart-open (7.0.4-2) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up r-cran-modelmetrics (1.2.2.2-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b4) ... Setting up python3-pulp (2.7.0+dfsg-4) ... /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:322: SyntaxWarning: invalid escape sequence '\ ' """ Setting up r-cran-matrixmodels (0.5-3-1) ... Setting up python3-charset-normalizer (3.4.0-1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b2) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-clock (0.7.1-1) ... Setting up r-cran-proc (1.18.5-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-yaml (6.0.2-1) ... Setting up python3-tk:amd64 (3.12.6-1) ... Setting up r-cran-survival (3.7-0-1) ... Setting up python3-gitdb (4.0.11-1) ... Setting up r-cran-future (1.34.0+dfsg-1) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up python3-yte (1.5.4-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-cran-future.apply (1.11.2+dfsg-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up r-cran-timechange (0.3.0-1) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-git (3.1.37-3) ... Setting up r-cran-gridextra (2.3-3) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-lava (1.7.3+dfsg-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-e1071 (1.7-16-1) ... Setting up r-cran-hardhat (1.4.0+dfsg-1) ... Setting up r-cran-dplyr (1.1.4-1) ... Setting up python3-referencing (0.35.1-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up r-cran-lubridate (1.9.3+dfsg-1) ... Setting up r-cran-prodlim (2024.06.25-1) ... Setting up python3-py (1.11.0-2) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up r-bioc-savr (1.37.0-4) ... Setting up r-cran-ipred (0.9-15-1) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up python3-retry (0.9.2-3) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up r-cran-recipes (1.1.0+dfsg-1) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-stopit (1.1.2-3) ... Setting up python3-contourpy (1.3.0-2) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-scipy (1.13.1-5) ... Setting up r-cran-caret (6.0-94+dfsg-1) ... Setting up python3-jsonschema (4.19.2-5) ... Setting up r-cran-conquer (1.3.3-1) ... Setting up r-cran-quantreg (5.99-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-fonttools (4.54.1-4) ... Setting up python3-matplotlib (3.8.3-3) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up snakemake (7.32.4-6) ... Setting up qcumber (2.3.0-2) ... ************************************************************************* * Minikraken DB is missing. Either move the according files to * * /var/lib/kraken/minikraken_20141208 * or call the script /usr/share/doc/qcumber/get-minikrakendb as root. * ************************************************************************* 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. 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-y', 'install', 'qcumber'] 0m58.7s INFO: Running scripts post_install 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_install_exceptions'] 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_install_exceptions'] 0m58.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 0m59.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 0m59.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmprwr7rloc to sid 0m59.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m59.9s INFO: Running scripts pre_distupgrade 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'update'] 1m2.1s 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 [7333 kB] Fetched 17.6 MB in 2s (10.0 MB/s) Reading package lists... 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'update'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-yf', 'dist-upgrade'] 1m8.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils gcc-14-base git git-man gpgv libatomic1 libaudit-common libaudit1 libblkid1 libdebconfclient0 libgcc-s1 libgfortran5 libgomp1 libmount1 libperl5.40 libpython3.12-minimal libpython3.12-stdlib libsmartcols1 libstdc++6 libsystemd0 libudev1 libuuid1 libx11-6 libx11-data login mount perl perl-base perl-modules-5.40 python3-attr python3-pkg-resources python3-smart-open python3.12 python3.12-minimal python3.12-tk r-base-core r-cran-dplyr r-cran-rcpp tzdata util-linux 40 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 64.3 MB of archives. After this operation, 896 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-10 [105 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-7 [4324 kB] Get:3 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-7 [267 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.0-7 [1675 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-7 [3017 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-10 [35.7 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-10 [168 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-10 [199 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-10 [139 kB] Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-10 [1217 kB] Get:11 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-10 [154 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-3 [12.4 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-3 [54.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-10 [81.4 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.7-2 [671 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.7-2 [2161 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.7-2 [1967 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.7-2 [815 kB] Get:19 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-3 [255 kB] Get:20 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.45-2 [219 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:22 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-8 [47.2 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-8 [714 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-8 [72.7 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.273 [10.1 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc1-3 [445 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc1-3 [146 kB] Get:30 http://deb.debian.org/debian sid/main amd64 git-man all 1:2.45.2-1.1 [2159 kB] Get:31 http://deb.debian.org/debian sid/main amd64 git amd64 1:2.45.2-1.1 [8662 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:34 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-smart-open all 7.0.5-1 [98.5 kB] Get:37 http://deb.debian.org/debian sid/main amd64 python3.12-tk amd64 3.12.7-2 [112 kB] Get:38 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:39 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-2 [1542 kB] Get:40 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 64.3 MB in 0s (226 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 ... 33268 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-10_amd64.deb ... Unpacking bsdutils (1:2.40.2-10) over (1:2.40.2-9) ... Setting up bsdutils (1:2.40.2-10) ... (Reading database ... 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Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-smart-open (7.0.5-1) ... Setting up python3.12-tk (3.12.7-2) ... Setting up libpython3.12-minimal:amd64 (3.12.7-2) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 7 15:29:44 UTC 2024. Universal Time is now: Thu Nov 7 15:29:44 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libx11-data (2:1.8.10-2) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up mount (2.40.2-10) ... Setting up perl-modules-5.40 (5.40.0-7) ... Setting up git-man (1:2.45.2-1.1) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up login (1:4.16.0-2+really2.40.2-10) ... Setting up python3.12-minimal (3.12.7-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-2) ... Setting up python3.12 (3.12.7-2) ... Setting up libperl5.40:amd64 (5.40.0-7) ... Setting up perl (5.40.0-7) ... Setting up r-base-core (4.4.2-1) ... Installing new version of config file /etc/R/Makeconf ... Setting up git (1:2.45.2-1.1) ... Setting up r-cran-dplyr (1.1.4-2) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Processing triggers for libc-bin (2.40-3) ... 1m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-yf', 'dist-upgrade'] 1m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m8.5s DUMP: a6fc1d88a982bddb9bc0255e931d8ccb - 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'show', '--no-all-versions', 'qcumber'] 1m8.6s DUMP: Package: qcumber Version: 2.3.0-2 Installed-Size: 236 Maintainer: Debian Med Packaging Team Architecture: all Replaces: qc-pipeline Provides: qc-pipeline Depends: python3:any, debconf (>= 0.5) | debconf-2.0, python3-jinja2, python3-matplotlib, python3-biopython, libjs-angularjs, libjs-bootstrap, libjs-d3, libjs-jquery, r-base-core, r-bioc-savr, r-cran-ggplot2, r-cran-quantreg, snakemake Conflicts: qc-pipeline Description-en: quality control of genomic sequences QCPipeline is a tool for quality control. The workflow is as follows: . 1. Quality control with FastQC 2. Trim Reads with Trimmomatic 3. Quality control of trimmed reads with FastQC 4. Map reads against reference using bowtie2 5. Classify reads with Kraken Description-md5: 380ba80499911de0a248a18cb1009872 Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber Section: science Priority: optional Filename: pool/main/q/qcumber/qcumber_2.3.0-2_all.deb Size: 50488 MD5sum: e8e75d1efdd4265bdbe9e121b7109314 SHA256: 033afeb7358c5e35109c648bbc275842755dc14c328f84007af5a389c06501cb 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'show', '--no-all-versions', 'qcumber'] 1m8.6s INFO: apt-cache knows about the following packages: qcumber 1m8.6s INFO: Running scripts pre_install 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_database-server'] 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_database-server'] 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_exceptions'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_exceptions'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_extras'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_extras'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy'] 1m8.7s 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: 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy', 'qcumber'] 1m8.7s DUMP: qcumber: Installed: 2.3.0-2 Candidate: 2.3.0-2 Version table: *** 2.3.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy', 'qcumber'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-y', 'install', 'qcumber'] 1m9.0s DUMP: Reading package lists... Building dependency tree... Reading state information... qcumber is already the newest version (2.3.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-y', 'install', 'qcumber'] 1m9.0s INFO: Running scripts post_install 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_install_exceptions'] 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_install_exceptions'] 1m9.0s INFO: Running scripts post_distupgrade 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_exceptions'] 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_exceptions'] 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_zz_backports'] 1m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_distupgrade_zz_backports'] 1m9.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m10.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m10.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m11.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m11.4s INFO: Running scripts pre_install 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_database-server'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_database-server'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_exceptions'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_exceptions'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_extras'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_extras'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy'] 1m11.4s 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: 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy', 'qcumber'] 1m11.4s DUMP: qcumber: Installed: 2.3.0-2 Candidate: 2.3.0-2 Version table: *** 2.3.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-cache', 'policy', 'qcumber'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-y', 'install', 'qcumber=2.3.0-2'] 1m11.7s DUMP: Reading package lists... Building dependency tree... Reading state information... qcumber is already the newest version (2.3.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', '-y', 'install', 'qcumber=2.3.0-2'] 1m11.7s INFO: Running scripts post_install 1m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_install_exceptions'] 1m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_install_exceptions'] 1m11.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m12.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m14.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', '-ac', '--ignore-obsolete'] 1m16.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', '-ac', '--ignore-obsolete'] 1m16.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m16.2s DUMP: 0.15.6 1m16.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m16.2s INFO: Running adequate version 0.15.6 now. 1m16.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'qcumber'] 1m16.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'qcumber'] 1m16.3s INFO: Running scripts pre_remove 1m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_exceptions'] 1m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/pre_remove_exceptions'] 1m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m19.2s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-10 install ok installed ca-certificates ca-certificates 20240203 install ok installed coinor-cbc coinor-cbc 2.10.12+ds-1 install ok installed coinor-libcbc3.1:amd64 coinor-libcbc3.1 2.10.12+ds-1 install ok installed coinor-libcgl1:amd64 coinor-libcgl1 0.60.9+ds-1 install ok installed coinor-libclp1:amd64 coinor-libclp1 1.17.10+ds-1 install ok installed coinor-libcoinutils3v5:amd64 coinor-libcoinutils3v5 2.11.11+ds-1+b1 install ok installed coinor-libosi1v5:amd64 coinor-libosi1v5 0.108.10+ds-1+b1 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 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed docutils-common docutils-common 0.21.2+dfsg-2 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 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 fonts-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed fonts-lyx fonts-lyx 2.4.2.1-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed git git 1:2.45.2-1.1 install ok installed git-man git-man 1:2.45.2-1.1 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 2.9.10 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 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libblas3:amd64 libblas3 3.12.0-3+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-10 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 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 libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.10.1-2 install ok installed libcurl4t64:amd64 libcurl4t64 8.10.1-2 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 0.273 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed liberror-perl liberror-perl 0.17029-2 install ok installed libexpat1:amd64 libexpat1 2.6.3-2 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+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 2.82.2-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 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 libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 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 libimagequant0:amd64 libimagequant0 2.18.0-1+b2 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 libjs-angularjs libjs-angularjs 1.8.3-1 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-d3 libjs-d3 3.5.17-4 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 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 3.12.0-3+b1 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 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 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 2.40.2-10 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 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 libnghttp3-9:amd64 libnghttp3-9 1.4.0-1+b1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b4 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 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 libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-7 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-2 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b2 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 2.5.5-1+b2 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-10 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 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 libsystemd0:amd64 libsystemd0 257~rc1-3 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 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 libtinfo6:amd64 libtinfo6 6.5-2+b1 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 libudev1:amd64 libudev1 257~rc1-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-10 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1+b1 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 1:1.1.2-3+b2 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 libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1+b1 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 libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-10 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-10 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 passwd passwd 1:4.16.0-4 install ok installed perl perl 5.40.0-7 install ok installed perl-base perl-base 5.40.0-7 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-7 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.12.6-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 24.2.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.84+dfsg-4 install ok installed python3-brotli python3-brotli 1.1.0-2+b5 install ok installed python3-cairo python3-cairo 1.26.1-2 install ok installed python3-certifi python3-certifi 2024.8.30+dfsg-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.0-1 install ok installed python3-configargparse python3-configargparse 1.7-1 install ok installed python3-connection-pool python3-connection-pool 0.0.3-2 install ok installed python3-contourpy python3-contourpy 1.3.0-2 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-datrie:amd64 python3-datrie 0.8.2-5 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-docutils python3-docutils 0.21.2+dfsg-2 install ok installed python3-dpath python3-dpath 2.2.0-1 install ok installed python3-fastjsonschema python3-fastjsonschema 2.20.0-1 install ok installed python3-fonttools python3-fonttools 4.54.1-4 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-git python3-git 3.1.37-3 install ok installed python3-gitdb python3-gitdb 4.0.11-1 install ok installed python3-humanfriendly python3-humanfriendly 10.0-6 install ok installed python3-idna python3-idna 3.8-2 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-jinja2 python3-jinja2 3.1.3-1 install ok installed python3-jsonschema python3-jsonschema 4.19.2-5 install ok installed python3-jsonschema-specifications python3-jsonschema-specifications 2023.12.1-2 install ok installed python3-jupyter-core python3-jupyter-core 5.7.2-4 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-2 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b4 install ok installed python3-markupsafe python3-markupsafe 2.1.5-1+b1 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-nbformat python3-nbformat 5.9.1-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 install ok installed python3-packaging python3-packaging 24.1-1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.4.0-1 install ok installed python3-pkg-resources python3-pkg-resources 75.2.0-1 install ok installed python3-plac python3-plac 1.4.3-1 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-psutil python3-psutil 5.9.8-2 install ok installed python3-pulp python3-pulp 2.7.0+dfsg-4 install ok installed python3-py python3-py 1.11.0-2 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-ratelimiter python3-ratelimiter 1.2.0.post0-4 install ok installed python3-referencing python3-referencing 0.35.1-1 install ok installed python3-reportlab python3-reportlab 4.2.5-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-retry python3-retry 0.9.2-3 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-roman python3-roman 4.2-1 install ok installed python3-rpds-py python3-rpds-py 0.20.1-1 install ok installed python3-scipy python3-scipy 1.13.1-5 install ok installed python3-six python3-six 1.16.0-7 install ok installed python3-smart-open python3-smart-open 7.0.5-1 install ok installed python3-smmap python3-smmap 6.0.0-1 install ok installed python3-stopit python3-stopit 1.1.2-3 install ok installed python3-sympy python3-sympy 1.13.3-1 install ok installed python3-tabulate python3-tabulate 0.9.0-1 install ok installed python3-throttler python3-throttler 1.2.2-2 install ok installed python3-tk:amd64 python3-tk 3.12.6-1 install ok installed python3-toposort python3-toposort 1.10-2 install ok installed python3-traitlets python3-traitlets 5.14.3+really5.14.3-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b2 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3-wrapt python3-wrapt 1.15.0-3 install ok installed python3-yaml python3-yaml 6.0.2-1 install ok installed python3-yte python3-yte 1.5.4-1 install ok installed python3.12 python3.12 3.12.7-2 install ok installed python3.12-minimal python3.12-minimal 3.12.7-2 install ok installed python3.12-tk python3.12-tk 3.12.7-2 install ok installed python3.13-tk python3.13-tk 3.13.0-1 install ok installed qcumber qcumber 2.3.0-2 install ok installed r-base-core r-base-core 4.4.2-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.50.0-2 install ok installed r-bioc-savr r-bioc-savr 1.37.0-4 install ok installed r-cran-caret r-cran-caret 6.0-94+dfsg-1 install ok installed r-cran-class r-cran-class 7.3-22-2 install ok installed r-cran-cli r-cran-cli 3.6.3-1 install ok installed r-cran-clock r-cran-clock 0.7.1-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-1+dfsg-1 install ok installed r-cran-conquer r-cran-conquer 1.3.3-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.5.0-1 install ok installed r-cran-data.table r-cran-data.table 1.16.2+dfsg-1 install ok installed r-cran-diagram r-cran-diagram 1.6.5-2 install ok installed r-cran-digest r-cran-digest 0.6.37-1 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-2 install ok installed r-cran-e1071 r-cran-e1071 1.7-16-1 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-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-future r-cran-future 1.34.0+dfsg-1 install ok installed r-cran-future.apply r-cran-future.apply 1.11.2+dfsg-1 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.5.1+dfsg-1 install ok installed r-cran-globals r-cran-globals 0.16.3-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gower r-cran-gower 1.0.1-1 install ok installed r-cran-gridextra r-cran-gridextra 2.3-3 install ok installed r-cran-gtable r-cran-gtable 0.3.6+dfsg-1 install ok installed r-cran-hardhat r-cran-hardhat 1.4.0+dfsg-1 install ok installed r-cran-ipred r-cran-ipred 0.9-15-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-24-1 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-lava r-cran-lava 1.7.3+dfsg-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-listenv r-cran-listenv 0.9.1+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-lubridate r-cran-lubridate 1.9.3+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-matrixmodels r-cran-matrixmodels 0.5-3-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.4.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-modelmetrics r-cran-modelmetrics 1.2.2.2-1+b1 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-nnet r-cran-nnet 7.3-19-2 install ok installed r-cran-numderiv r-cran-numderiv 2016.8-1.1-3 install ok installed r-cran-parallelly r-cran-parallelly 1.38.0-1 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-pkgkitten r-cran-pkgkitten 0.2.4-1 install ok installed r-cran-plyr r-cran-plyr 1.8.9-1 install ok installed r-cran-proc r-cran-proc 1.18.5-1 install ok installed r-cran-prodlim r-cran-prodlim 2024.06.25-1 install ok installed r-cran-progressr r-cran-progressr 0.14.0-1 install ok installed r-cran-proxy r-cran-proxy 0.4-27-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 install ok installed r-cran-quantreg r-cran-quantreg 5.99-1 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-rcpp r-cran-rcpp 1.0.13-1-1 install ok installed r-cran-rcpparmadillo r-cran-rcpparmadillo 14.0.2-1-1 install ok installed r-cran-recipes r-cran-recipes 1.1.0+dfsg-1 install ok installed r-cran-reshape2 r-cran-reshape2 1.4.4-2 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-rpart r-cran-rpart 4.1.23-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-shape r-cran-shape 1.4.6.1-1 install ok installed r-cran-sparsem r-cran-sparsem 1.84-2-1+b1 install ok installed r-cran-squarem r-cran-squarem 2021.1-1 install ok installed r-cran-stringi r-cran-stringi 1.8.4-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-survival r-cran-survival 3.7-0-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.1+dfsg-1 install ok installed r-cran-timechange r-cran-timechange 0.3.0-1 install ok installed r-cran-timedate r-cran-timedate 4041.110-1 install ok installed r-cran-tzdb r-cran-tzdb 0.4.0-2 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 r-cran-xml r-cran-xml 3.99-0.17-1 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sgml-base sgml-base 1.31 install ok installed snakemake snakemake 7.32.4-6 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024b-3 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.1.0-1 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 2.40.2-10 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 1m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'remove', 'blt', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-urw-base35', 'git', 'git-man', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-angularjs', 'libjs-bootstrap', 'libjs-d3', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'littler', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-markupsafe', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-retry', 'python3-rlpycairo', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-savr', 'r-cran-caret', 'r-cran-class', 'r-cran-cli', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-conquer', 'r-cran-cpp11', 'r-cran-data.table', 'r-cran-diagram', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-e1071', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-modelmetrics', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-parallelly', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progressr', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-recipes', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-rpart', 'r-cran-scales', 'r-cran-shape', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'r-cran-xml', 'readline-common', 'sensible-utils', 'sgml-base', 'snakemake', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip', 'qcumber'] 1m43.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt ca-certificates coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-lyx fonts-urw-base35 git git-man libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 liberror-perl libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-angularjs libjs-bootstrap libjs-d3 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-0-2 littler media-types netbase openssl perl perl-modules-5.40 python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-configargparse python3-connection-pool python3-contourpy python3-cycler python3-dateutil python3-datrie python3-decorator python3-docutils python3-dpath python3-fastjsonschema python3-fonttools python3-freetype python3-fs python3-git python3-gitdb python3-humanfriendly python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbformat python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-plac python3-platformdirs python3-psutil python3-pulp python3-py python3-pyparsing python3-ratelimiter python3-referencing python3-reportlab python3-requests python3-retry python3-rlpycairo python3-roman python3-rpds-py python3-scipy python3-six python3-smart-open python3-smmap python3-stopit python3-sympy python3-tabulate python3-throttler python3-tk python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wrapt python3-yaml python3-yte python3.12 python3.12-minimal python3.12-tk python3.13-tk qcumber r-base-core r-bioc-biocgenerics r-bioc-savr r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cpp11 r-cran-data.table r-cran-diagram r-cran-digest r-cran-dplyr r-cran-e1071 r-cran-fansi r-cran-farver r-cran-foreach r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gridextra r-cran-gtable r-cran-hardhat r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-mgcv r-cran-modelmetrics r-cran-munsell r-cran-nlme r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-recipes r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-scales r-cran-shape r-cran-sparsem r-cran-squarem r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xml readline-common sensible-utils sgml-base snakemake tk8.6-blt2.5 ucf unicode-data unzip w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 0 upgraded, 0 newly installed, 310 to remove and 0 not upgraded. After this operation, 701 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 ... 33256 files and directories currently installed.) Removing qcumber (2.3.0-2) ... Removing python3-biopython (1.84+dfsg-4) ... Removing python3-reportlab (4.2.5-1) ... Removing python3-matplotlib (3.8.3-3) ... Removing python3-pil.imagetk:amd64 (10.4.0-1) ... Removing python3-pil:amd64 (10.4.0-1) ... Removing python3-tk:amd64 (3.12.6-1) ... Removing blt (2.5.3+dfsg-7) ... Removing snakemake (7.32.4-6) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing python3-pulp (2.7.0+dfsg-4) ... Removing coinor-cbc (2.10.12+ds-1) ... Removing coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Removing coinor-libcgl1:amd64 (0.60.9+ds-1) ... Removing coinor-libclp1:amd64 (1.17.10+ds-1) ... Removing coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Removing coinor-libcoinutils3v5:amd64 (2.11.11+ds-1+b1) ... Removing python3-docutils (0.21.2+dfsg-2) ... Removing docutils-common (0.21.2+dfsg-2) ... Removing r-cran-quantreg (5.99-1) ... Removing r-cran-conquer (1.3.3-1) ... Removing r-cran-caret (6.0-94+dfsg-1) ... Removing r-cran-recipes (1.1.0+dfsg-1) ... Removing r-cran-ipred (0.9-15-1) ... Removing r-cran-rpart (4.1.23-1) ... Removing r-cran-prodlim (2024.06.25-1) ... Removing r-cran-matrixmodels (0.5-3-1) ... Removing r-bioc-savr (1.37.0-4) ... Removing r-cran-reshape2 (1.4.4-2) ... Removing r-cran-rcpparmadillo (14.0.2-1-1) ... Removing r-cran-ggplot2 (3.5.1+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.0-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing fonts-lyx (2.4.2.1-1) ... Removing python3-git (3.1.37-3) ... Removing git (1:2.45.2-1.1) ... Removing git-man (1:2.45.2-1.1) ... Removing libraqm0:amd64 (0.10.1-1+b2) ... Removing python3-contourpy (1.3.0-2) ... Removing r-cran-mgcv (1.9-1-1) ... Removing python3-freetype (2.5.1-1) ... Removing libcurl3t64-gnutls:amd64 (8.10.1-2) ... Removing python3-datrie:amd64 (0.8.2-5) ... Removing liberror-perl (0.17029-2) ... Removing python3-nbformat (5.9.1-1) ... Removing python3-jsonschema (4.19.2-5) ... Removing python3-jsonschema-specifications (2023.12.1-2) ... Removing python3-referencing (0.35.1-1) ... Removing python3-rpds-py (0.20.1-1) ... Removing python3-yte (1.5.4-1) ... Removing python3-stopit (1.1.2-3) ... Removing python3-retry (0.9.2-3) ... Removing python3-py (1.11.0-2) ... Removing python3-humanfriendly (10.0-6) ... Removing python3-yaml (6.0.2-1) ... Removing python3-jupyter-core (5.7.2-4) ... Removing python3-traitlets (5.14.3+really5.14.3-1) ... Removing perl (5.40.0-7) ... Removing libperl5.40:amd64 (5.40.0-7) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing r-cran-gower (1.0.1-1) ... Removing r-cran-modelmetrics (1.2.2.2-1+b1) ... Removing r-cran-data.table (1.16.2+dfsg-1) ... Removing r-cran-tidyr (1.3.1-1) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-stringi (1.8.4-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libjs-angularjs (1.8.3-1) ... Removing libjs-d3 (3.5.17-4) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libnghttp3-9:amd64 (1.4.0-1+b1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libwebpmux3:amd64 (1.4.0-0.1+b1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Removing python3.12-tk (3.12.7-2) ... Removing libyaml-0-2:amd64 (0.2.5-1+b2) ... Removing littler (0.3.20-1) ... Removing perl-modules-5.40 (5.40.0-7) ... Removing python3-certifi (2024.8.30+dfsg-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-charset-normalizer (3.4.0-1) ... Removing python3-configargparse (1.7-1) ... Removing python3-connection-pool (0.0.3-2) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-dpath (2.2.0-1) ... Removing python3-fastjsonschema (2.20.0-1) ... Removing python3-gitdb (4.0.11-1) ... Removing python3-idna (3.8-2) ... Removing python3-jinja2 (3.1.3-1) ... Removing python3-kiwisolver (1.4.7-2) ... Removing python3-markupsafe (2.1.5-1+b1) ... Removing python3-packaging (24.1-1) ... Removing python3-plac (1.4.3-1) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-psutil (5.9.8-2) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-ratelimiter (1.2.0.post0-4) ... Removing python3-roman (4.2-1) ... Removing python3-smart-open (7.0.5-1) ... Removing python3-smmap (6.0.0-1) ... Removing python3-tabulate (0.9.0-1) ... Removing python3-throttler (1.2.2-2) ... Removing python3-toposort (1.10-2) ... Removing python3-urllib3 (2.0.7-2) ... Removing python3-wrapt (1.15.0-3) ... Removing r-bioc-biocgenerics (0.50.0-2) ... Removing r-cran-e1071 (1.7-16-1) ... Removing r-cran-class (7.3-22-2) ... Removing r-cran-dplyr (1.1.4-2) ... Removing r-cran-tidyselect (1.2.1+dfsg-1) ... Removing r-cran-hardhat (1.4.0+dfsg-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-clock (0.7.1-1) ... Removing r-cran-lava (1.7.3+dfsg-1) ... Removing r-cran-future.apply (1.11.2+dfsg-1) ... Removing r-cran-future (1.34.0+dfsg-1) ... Removing r-cran-globals (0.16.3-1) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-munsell (0.5.1-1) ... Removing r-cran-colorspace (2.1-1+dfsg-1) ... Removing r-cran-tzdb (0.4.0-2) ... Removing r-cran-lubridate (1.9.3+dfsg-1) ... Removing r-cran-timechange (0.3.0-1) ... Removing r-cran-cpp11 (0.5.0-1) ... Removing r-cran-diagram (1.6.5-2) ... Removing r-cran-progressr (0.14.0-1) ... Removing r-cran-digest (0.6.37-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.2-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-gridextra (2.3-3) ... Removing r-cran-gtable (0.3.6+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-iterators (1.0.14-1) ... Removing r-cran-kernsmooth (2.23-24-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.166-1) ... Removing r-cran-listenv (0.9.1+dfsg-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-61-1) ... Removing r-cran-matrixstats (1.4.1-1) ... Removing r-cran-nnet (7.3-19-2) ... Removing r-cran-numderiv (2016.8-1.1-3) ... Removing r-cran-parallelly (1.38.0-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-proc (1.18.5-1) ... Removing r-cran-plyr (1.8.9-1) ... Removing r-cran-proxy (0.4-27-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-shape (1.4.6.1-1) ... Removing r-cran-sparsem (1.84-2-1+b1) ... Removing r-cran-squarem (2021.1-1) ... Removing r-cran-timedate (4041.110-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-withr (3.0.2+dfsg-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing r-cran-survival (3.7-0-1) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-cran-rcpp (1.0.13-1-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-cli (3.6.3-1) ... 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-urw-base35 (20200910-8) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-2) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing xfonts-utils (1:7.7+7) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.10.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b5) ... 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 libfontenc1:amd64 (1:1.1.8-1+b1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... 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 libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... 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 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... 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 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 ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-14) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. 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 (1:1.1.2-3+b2) ... Removing openssl (3.3.2-2) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... Removing python3-attr (24.2.0-1) ... Removing python3-fonttools (4.54.1-4) ... Removing python3-scipy (1.13.1-5) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-3+b1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing python3-lxml:amd64 (5.3.0-1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing python3-fs (2.4.16-4) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-brotli (1.1.0-2+b5) ... Removing python3-decorator (5.1.1-5) ... Removing python3-lz4 (4.0.2+dfsg-1+b4) ... Removing python3-sympy (1.13.3-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-six (1.16.0-7) ... Removing python3-tz (2024.1-2) ... Removing python3-unicodedata2 (15.1.0+ds-1+b2) ... Removing unicode-data (15.1.0-1) ... Removing libblas3:amd64 (3.12.0-3+b1) ... Removing python3-pkg-resources (75.2.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3 (3.12.6-1) ... Removing python3.12 (3.12.7-2) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12-minimal (3.12.7-2) ... Removing libexpat1:amd64 (2.6.3-2) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... 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 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 libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 1m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'remove', 'blt', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-urw-base35', 'git', 'git-man', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-angularjs', 'libjs-bootstrap', 'libjs-d3', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'littler', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-markupsafe', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-retry', 'python3-rlpycairo', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-savr', 'r-cran-caret', 'r-cran-class', 'r-cran-cli', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-conquer', 'r-cran-cpp11', 'r-cran-data.table', 'r-cran-diagram', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-e1071', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-modelmetrics', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-parallelly', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progressr', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-recipes', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-rpart', 'r-cran-scales', 'r-cran-shape', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'r-cran-xml', 'readline-common', 'sensible-utils', 'sgml-base', 'snakemake', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip', 'qcumber'] 1m43.4s INFO: Running scripts post_remove 1m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_remove_exceptions'] 1m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_remove_exceptions'] 1m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--purge', 'blt', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-urw-base35', 'git', 'git-man', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-angularjs', 'libjs-bootstrap', 'libjs-d3', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'littler', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-markupsafe', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-retry', 'python3-rlpycairo', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-savr', 'r-cran-caret', 'r-cran-class', 'r-cran-cli', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-conquer', 'r-cran-cpp11', 'r-cran-data.table', 'r-cran-diagram', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-e1071', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-modelmetrics', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-parallelly', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progressr', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-recipes', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-rpart', 'r-cran-scales', 'r-cran-shape', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'r-cran-xml', 'readline-common', 'sensible-utils', 'sgml-base', 'snakemake', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip'] 1m43.7s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5239 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 coinor-cbc which isn't installed dpkg: warning: ignoring request to remove coinor-libcbc3.1 which isn't installed dpkg: warning: ignoring request to remove coinor-libcgl1 which isn't installed dpkg: warning: ignoring request to remove coinor-libclp1 which isn't installed dpkg: warning: ignoring request to remove coinor-libcoinutils3v5 which isn't installed dpkg: warning: ignoring request to remove coinor-libosi1v5 which isn't installed Purging configuration files for docutils-common (0.21.2+dfsg-2) ... 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 fonts-glyphicons-halflings which isn't installed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... Purging configuration files for git (1:2.45.2-1.1) ... dpkg: warning: ignoring request to remove git-man which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 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 liberror-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.2-2) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-angularjs which isn't installed dpkg: warning: ignoring request to remove libjs-bootstrap which isn't installed dpkg: warning: ignoring request to remove libjs-d3 which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove 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 libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-2) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 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 libtcl8.6 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 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 libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 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 libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for perl (5.40.0-7) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.12.6-1) ... dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-configargparse which isn't installed dpkg: warning: ignoring request to remove python3-connection-pool which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-datrie which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-docutils which isn't installed dpkg: warning: ignoring request to remove python3-dpath which isn't installed dpkg: warning: ignoring request to remove python3-fastjsonschema which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-git which isn't installed dpkg: warning: ignoring request to remove python3-gitdb which isn't installed dpkg: warning: ignoring request to remove python3-humanfriendly which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-jinja2 which isn't installed Purging configuration files for python3-jsonschema (4.19.2-5) ... dpkg: warning: ignoring request to remove python3-jsonschema-specifications which isn't installed dpkg: warning: ignoring request to remove python3-jupyter-core which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-markupsafe which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-nbformat which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-plac which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-psutil which isn't installed dpkg: warning: ignoring request to remove python3-pulp which isn't installed dpkg: warning: ignoring request to remove python3-py which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-ratelimiter which isn't installed dpkg: warning: ignoring request to remove python3-referencing which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-retry which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-roman which isn't installed dpkg: warning: ignoring request to remove python3-rpds-py which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-smart-open which isn't installed dpkg: warning: ignoring request to remove python3-smmap which isn't installed dpkg: warning: ignoring request to remove python3-stopit which isn't installed Purging configuration files for python3-sympy (1.13.3-1) ... dpkg: warning: ignoring request to remove python3-tabulate which isn't installed dpkg: warning: ignoring request to remove python3-throttler which isn't installed dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-toposort which isn't installed dpkg: warning: ignoring request to remove python3-traitlets which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wrapt which isn't installed dpkg: warning: ignoring request to remove python3-yaml which isn't installed dpkg: warning: ignoring request to remove python3-yte which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-2) ... dpkg: warning: ignoring request to remove python3.12-tk which isn't installed dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for r-base-core (4.4.2-1) ... dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-savr which isn't installed dpkg: warning: ignoring request to remove r-cran-caret which isn't installed dpkg: warning: ignoring request to remove r-cran-class which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-clock which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools 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-conquer which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-data.table which isn't installed dpkg: warning: ignoring request to remove r-cran-diagram which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-e1071 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-foreach which isn't installed dpkg: warning: ignoring request to remove r-cran-future which isn't installed dpkg: warning: ignoring request to remove r-cran-future.apply which isn't installed dpkg: warning: ignoring request to remove r-cran-generics 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-globals 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-gower which isn't installed dpkg: warning: ignoring request to remove r-cran-gridextra 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-hardhat which isn't installed dpkg: warning: ignoring request to remove r-cran-ipred 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-iterators which isn't installed dpkg: warning: ignoring request to remove r-cran-kernsmooth 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-lava 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-listenv which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-lubridate 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-matrixmodels which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats 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-modelmetrics 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-nnet which isn't installed dpkg: warning: ignoring request to remove r-cran-numderiv which isn't installed dpkg: warning: ignoring request to remove r-cran-parallelly 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-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plyr which isn't installed dpkg: warning: ignoring request to remove r-cran-proc which isn't installed dpkg: warning: ignoring request to remove r-cran-prodlim which isn't installed dpkg: warning: ignoring request to remove r-cran-progressr which isn't installed dpkg: warning: ignoring request to remove r-cran-proxy which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-quantreg 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-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpparmadillo which isn't installed dpkg: warning: ignoring request to remove r-cran-recipes which isn't installed dpkg: warning: ignoring request to remove r-cran-reshape2 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-rpart 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-shape which isn't installed dpkg: warning: ignoring request to remove r-cran-sparsem which isn't installed dpkg: warning: ignoring request to remove r-cran-squarem which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-survival 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-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-timechange which isn't installed dpkg: warning: ignoring request to remove r-cran-timedate which isn't installed dpkg: warning: ignoring request to remove r-cran-tzdb 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 dpkg: warning: ignoring request to remove r-cran-xml 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 sgml-base (1.31) ... dpkg: warning: ignoring request to remove snakemake which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for unzip (6.0-28) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... dpkg: warning: ignoring request to remove zip which isn't installed 1m43.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--purge', 'blt', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-urw-base35', 'git', 'git-man', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-angularjs', 'libjs-bootstrap', 'libjs-d3', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'littler', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-markupsafe', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-reportlab', 'python3-requests', 'python3-retry', 'python3-rlpycairo', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-savr', 'r-cran-caret', 'r-cran-class', 'r-cran-cli', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-conquer', 'r-cran-cpp11', 'r-cran-data.table', 'r-cran-diagram', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-e1071', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-modelmetrics', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-parallelly', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progressr', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-recipes', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-rpart', 'r-cran-scales', 'r-cran-shape', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-withr', 'r-cran-xml', 'readline-common', 'sensible-utils', 'sgml-base', 'snakemake', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip'] 1m43.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--purge', 'qcumber'] 1m43.8s DUMP: (Reading database ... 5163 files and directories currently installed.) Purging configuration files for qcumber (2.3.0-2) ... 1m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--purge', 'qcumber'] 1m43.8s INFO: Running scripts post_purge 1m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_purge_exceptions'] 1m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_purge_exceptions'] 1m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--purge', '--pending'] 1m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--purge', '--pending'] 1m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--remove', '--pending'] 1m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg', '--remove', '--pending'] 1m43.8s INFO: Running scripts post_test 1m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_test_exceptions'] 1m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'tmp/scripts/post_test_exceptions'] 1m43.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m44.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m44.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg-divert', '--list'] 1m44.0s 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 1m44.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'dpkg-divert', '--list'] 1m44.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'clean'] 1m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprwr7rloc', 'apt-get', 'clean'] 1m44.1s DEBUG: Recording chroot state 1m44.4s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 1m44.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/shm'] 1m44.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/shm'] 1m44.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/console'] 1m44.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/console'] 1m44.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/ptmx'] 1m44.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/ptmx'] 1m44.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/pts'] 1m44.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/dev/pts'] 1m44.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/proc'] 1m44.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprwr7rloc/proc'] 1m44.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m44.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprwr7rloc'] 1m44.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmprwr7rloc 1m44.8s INFO: PASS: Upgrading between Debian distributions. 1m44.8s INFO: PASS: All tests. 1m44.8s INFO: piuparts run ends. ret=0 End: 2024-11-07 15:30:22 GMT