Start: 2025-02-06 21:56:38 GMT [testing] Package: cnvkit Version: 0.9.10-2 Installed-Size: 94731 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description: Copy number variant detection from targeted DNA sequencing Homepage: https://cnvkit.readthedocs.org Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.10-2_all.deb Size: 19501620 MD5sum: 34bc5101407f83474714510d690c42f5 SHA256: bf1fd75c757a204fb8123b69285b16b389dfc0c840d3941227ff8c7f89a602e3 [sid] Package: cnvkit Version: 0.9.12-1 Installed-Size: 94677 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate (>= 0.15), python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description: Copy number variant detection from targeted DNA sequencing Homepage: https://cnvkit.readthedocs.org Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.12-1_all.deb Size: 19867944 MD5sum: 1bab2eed9e247c45124199c37a680e14 SHA256: ae91c2bce847494e0e295aad3888522f2575eef877bd24355d13ac8236ceac8a 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 cnvkit=0.9.12-1 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 cnvkit=0.9.12-1 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/tmpczag7hcq 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpczag7hcq 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', '--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/tmpczag7hcq', '--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/tmpczag7hcq/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/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/tmpczag7hcq/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/tmpczag7hcq/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/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/tmpczag7hcq/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9418 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6315 kB] Fetched 15.9 MB in 1s (19.0 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt bsdutils dash dpkg libapt-pkg6.0t64 libblkid1 liblz4-1 libmount1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libselinux1 libsemanage-common libsemanage2 libsmartcols1 libuuid1 libxxhash0 login mount util-linux 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7100 kB of archives. After this operation, 334 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.4-2 [106 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-12 [98.5 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.10.0-3 [63.8 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.26 [1115 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.14 [1537 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.4-2 [36.3 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.4-2 [169 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.4-2 [199 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.4-2 [140 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.4-2 [1213 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.4-2 [155 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.7-3.1 [76.8 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.26 [1433 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libpam0g amd64 1.7.0-2 [69.8 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libpam-modules-bin amd64 1.7.0-2 [48.8 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libpam-modules amd64 1.7.0-2 [177 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libpam-runtime all 1.7.0-2 [248 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.4-2 [88.4 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.7-2.1 [7208 B] Get:21 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.7-2.1 [91.2 kB] Preconfiguring packages ... Fetched 7100 kB in 0s (64.4 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 ... 5029 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.4-2_amd64.deb ... Unpacking bsdutils (1:2.40.4-2) over (1:2.40.4-1) ... Setting up bsdutils (1:2.40.4-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5028 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.26_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.26) over (2.9.23) ... Setting up libapt-pkg6.0t64:amd64 (2.9.26) ... (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 ... 5028 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.14_amd64.deb ... Unpacking dpkg (1.22.14) over (1.22.11) ... Setting up dpkg (1.22.14) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5027 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.4-2_amd64.deb ... Unpacking libblkid1:amd64 (2.40.4-2) over (2.40.4-1) ... Setting up libblkid1:amd64 (2.40.4-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5027 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.4-2_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.4-2) over (2.40.4-1) ... Setting up libsmartcols1:amd64 (2.40.4-2) ... (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 ... 5027 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.4-2_amd64.deb ... Unpacking util-linux (2.40.4-2) over (2.40.4-1) ... Setting up util-linux (2.40.4-2) ... (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 ... 5027 files and directories currently installed.) Preparing to unpack .../mount_2.40.4-2_amd64.deb ... Unpacking mount (2.40.4-2) over (2.40.4-1) ... Preparing to unpack .../libselinux1_3.7-3.1_amd64.deb ... Unpacking libselinux1:amd64 (3.7-3.1) over (3.7-3+b1) ... Setting up libselinux1:amd64 (3.7-3.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5025 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.7.0-2_amd64.deb ... Unpacking libpam-modules-bin (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam-modules-bin (1.7.0-2) ... (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 ... 5016 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.7.0-2_amd64.deb ... Unpacking libpam-modules:amd64 (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam-modules:amd64 (1.7.0-2) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/namespace.init ... Installing new version of config file /etc/security/pwhistory.conf ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5025 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.40.4-2_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.4-2) over (1:4.16.0-2+really2.40.4-1) ... Preparing to unpack .../libsemanage-common_3.7-2.1_all.deb ... Unpacking libsemanage-common (3.7-2.1) over (3.7-2) ... Preparing to unpack .../libsemanage2_3.7-2.1_amd64.deb ... Unpacking libsemanage2:amd64 (3.7-2.1) over (3.7-2+b1) ... Setting up libsemanage-common (3.7-2.1) ... Setting up mount (2.40.4-2) ... Setting up libsemanage2:amd64 (3.7-2.1) ... Setting up login (1:4.16.0-2+really2.40.4-2) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.40-6) ... 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.8s DUMP: 61fcd4276162a3aacb2a7a941a2a67e8 - 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.8s INFO: Running scripts post_setup 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s 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 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.2s 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' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_minimize'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_minimize'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_zz_backports'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_setup_zz_backports'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DUMP: install ok installed apt apt 2.9.26 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.4-2 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.14 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-12 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.26 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblkid1:amd64 libblkid1 2.40.4-2 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 2.40-6 install ok installed libc6:amd64 libc6 2.40-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-12 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 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 2.40.4-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-2 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-2 install ok installed libpam-runtime libpam-runtime 1.7.0-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3.1 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-2 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-12 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libuuid1:amd64 libuuid1 2.40.4-2 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-2 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.4-2 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 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2024b-6 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-2 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 0m4.4s INFO: Running scripts is_testable 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s INFO: Running scripts pre_test 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_test_root_password'] 0m4.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_test_root_password'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m4.6s DUMP: Package: cnvkit Version: 0.9.10-2 Installed-Size: 94731 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description-en: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Homepage: https://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.10-2_all.deb Size: 19501620 MD5sum: 34bc5101407f83474714510d690c42f5 SHA256: bf1fd75c757a204fb8123b69285b16b389dfc0c840d3941227ff8c7f89a602e3 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m4.6s INFO: apt-cache knows about the following packages: cnvkit 0m4.6s INFO: Running scripts pre_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy'] 0m4.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy', 'cnvkit'] 0m4.6s DUMP: cnvkit: Installed: (none) Candidate: 0.9.10-2 Version table: 0.9.10-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy', 'cnvkit'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-y', 'install', 'cnvkit'] 0m52.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libunistring5 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 media-types netbase openssl procps python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-yaml python3-zipp python3.12-tk python3.13 python3.13-minimal python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common sensible-utils sgml-base 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 rng-tools low-memory-monitor gnutls-bin krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 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-cycler-doc python-joblib-doc 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-pandas-doc python3-statsmodels python-pil-doc python3-setuptools python-pomegranate-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-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-s4arrays r-bioc-sparsearray r-bioc-delayedarray r-bioc-hdf5array r-bioc-genomicranges r-bioc-pwalign r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit readline-doc sgml-base-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules psmisc linux-sysctl-defaults python-biopython-doc ncbi-blast+ python3-pytest python3-psutil python3-bs4 python3-cssselect python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-jinja2 python3-numba python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-pooch isympy-common r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: blt ca-certificates cnvkit fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libunistring5 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 media-types netbase openssl procps python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-yaml python3-zipp python3.12-tk python3.13 python3.13-minimal python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common sensible-utils sgml-base tk8.6-blt2.5 ucf unicode-data unzip w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 0 upgraded, 189 newly installed, 0 to remove and 0 not upgraded. Need to get 203 MB of archives. After this operation, 927 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.1-3+b1 [859 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.1-3+b1 [2203 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.1-3+b1 [1973 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.1-3+b1 [740 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:23 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:24 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0049 [42.5 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:36 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:50 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.8-5+b1 [113 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.1-3+b1 [104 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.13.1-1 [9464 B] Get:58 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1.1 [79.6 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-12 [137 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-12 [9300 B] Get:66 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1.1 [522 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:86 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.84+dfsg-4+b2 [1651 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-6 [95.1 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-4 [20.5 MB] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 python3-attr all 24.3.0-1 [68.8 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.55.3-2 [1633 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-3 [76.9 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b3 [5650 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-7 [7295 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-7 [3097 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-6 [216 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 8.6.1-1 [21.4 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:134 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:137 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-pomegranate amd64 0.14.8-7 [4256 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:149 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-7+b1 [6465 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 python3-sklearn all 1.4.2+dfsg-7 [2248 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:187 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 r-bioc-dnacopy amd64 1.80.0-2 [498 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 cnvkit all 0.9.10-2 [19.5 MB] Preconfiguring packages ... 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Setting up media-types (10.1.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libgpg-error0:amd64 (1.51-3) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.3-1) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-12) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up unicode-data (15.1.0-1) ... Setting up zip (3.0-14) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-3) ... Setting up libatomic1:amd64 (14.2.0-12) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-12) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up procps (2:4.0.4-7) ... Setting up libtasn1-6:amd64 (4.19.0-3+b3) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libpaper2:amd64 (2.2.5-0.3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.4.0-2) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up ucf (3.0049) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3+b1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.1-3+b1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up python3.12-tk (3.12.8-5+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-3+b1) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-tz (2024.2-1) ... Setting up python3-fs (2.4.16-6) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-cycler (0.12.1-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up python3-kiwisolver (1.4.7-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-contourpy (1.3.1-1) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.3.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-scipy (1.14.1-4) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-importlib-metadata (8.6.1-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:amd64 (8.11.1-1+b1) ... Setting up python3-joblib (1.3.2-6) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-7) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-7+b1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up python3-tk:amd64 (3.13.1-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (10.4.0-1.1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pandas (2.2.3+dfsg-7) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1.1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up python3-sklearn (1.4.2+dfsg-7) ... Setting up python3-reportlab (4.2.5-1) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-pyfaidx (0.8.1.3-1) ... Setting up r-bioc-biocgenerics (0.52.0-2) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up python3-networkx (3.2.1-5) ... Setting up r-bioc-dnacopy (1.80.0-2) ... Setting up python3-pomegranate (0.14.8-7) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-fonttools (4.55.3-2) ... Setting up python3-matplotlib (3.8.3-3+b3) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b2) ... Setting up cnvkit (0.9.10-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-y', 'install', 'cnvkit'] 0m52.3s INFO: Running scripts post_install 0m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_install_exceptions'] 0m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_install_exceptions'] 0m52.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 0m53.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 0m53.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpczag7hcq to sid 0m53.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m53.2s INFO: Running scripts pre_distupgrade 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'update'] 0m55.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 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 [7346 kB] Fetched 17.6 MB in 1s (12.4 MB/s) Reading package lists... 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'update'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-yf', 'dist-upgrade'] 1m6.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: cython3 python3-numpy-dev The following packages will be upgraded: apt bsdutils cnvkit dpkg gcc-14-base libapt-pkg6.0t64 libatomic1 libblkid1 libgcc-s1 libgfortran5 libglib2.0-0t64 libgomp1 libmount1 libncursesw6 libopenjp2-7 libpcre2-8-0 libpng16-16t64 libpython3.13-minimal libpython3.13-stdlib libselinux1 libsepol2 libsmartcols1 libstdc++6 libtinfo6 libuuid1 login mawk media-types mount ncurses-base ncurses-bin python3-biopython python3-numpy python3-pil python3-pil.imagetk python3-pomegranate python3-sympy python3.12-tk python3.13 python3.13-minimal python3.13-tk sqv tzdata util-linux 44 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 60.3 MB of archives. After this operation, 25.1 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-3 [106 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-16 [9296 B] Get:3 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-16 [137 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get:5 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-16 [48.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-16 [72.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-16 [713 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.27 [1120 kB] Get:9 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.15 [1537 kB] Get:10 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20250125-2 [438 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-3 [36.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.4-3 [169 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.4-3 [200 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-3 [140 kB] Get:15 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-3 [1214 kB] Get:16 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-3 [155 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.8-1 [84.3 kB] Get:19 http://deb.debian.org/debian sid/main amd64 sqv amd64 1.2.1-6 [623 kB] Get:20 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.27 [1440 kB] Get:21 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20250125-2 [273 kB] Get:22 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-3 [88.5 kB] Get:23 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get:27 http://deb.debian.org/debian sid/main amd64 media-types all 11.0.0 [27.6 kB] Get:28 http://deb.debian.org/debian sid/main amd64 tzdata all 2025a-2 [259 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20250125-2 [348 kB] Get:31 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB] Get:32 http://deb.debian.org/debian sid/main amd64 cython3 amd64 3.0.11+dfsg-1+b1 [3157 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-pomegranate amd64 0.15.0-1 [4263 kB] Get:34 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.85+dfsg-2 [1674 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.2+ds-2 [7507 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.2+ds-2 [138 kB] Get:37 http://deb.debian.org/debian sid/main amd64 cnvkit all 0.9.12-1 [19.9 MB] Get:38 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.8-1 [296 kB] Get:42 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 11.1.0-5 [81.5 kB] Get:43 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 11.1.0-5 [531 kB] Get:44 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-2 [4148 kB] Get:45 http://deb.debian.org/debian sid/main amd64 python3.12-tk amd64 3.12.9-1 [113 kB] Get:46 http://deb.debian.org/debian sid/main amd64 python3.13-tk amd64 3.13.2-1 [103 kB] Preconfiguring packages ... Fetched 60.3 MB in 0s (138 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 ... 25400 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.4-3_amd64.deb ... Unpacking bsdutils (1:2.40.4-3) over (1:2.40.4-2) ... Setting up bsdutils (1:2.40.4-3) ... (Reading database ... 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Unpacking libpng16-16t64:amd64 (1.6.46-4) over (1.6.44-3) ... Preparing to unpack .../10-libsepol2_3.8-1_amd64.deb ... Unpacking libsepol2:amd64 (3.8-1) over (3.7-1) ... Preparing to unpack .../11-python3-pil.imagetk_11.1.0-5_amd64.deb ... Unpacking python3-pil.imagetk:amd64 (11.1.0-5) over (10.4.0-1.1) ... Preparing to unpack .../12-python3-pil_11.1.0-5_amd64.deb ... Unpacking python3-pil:amd64 (11.1.0-5) over (10.4.0-1.1) ... Preparing to unpack .../13-python3-sympy_1.13.3-2_all.deb ... Unpacking python3-sympy (1.13.3-2) over (1.13.3-1) ... Preparing to unpack .../14-python3.12-tk_3.12.9-1_amd64.deb ... Unpacking python3.12-tk (3.12.9-1) over (3.12.8-5+b1) ... Preparing to unpack .../15-python3.13-tk_3.13.2-1_amd64.deb ... Unpacking python3.13-tk (3.13.2-1) over (3.13.1-3+b1) ... Setting up media-types (11.0.0) ... Installing new version of config file /etc/mime.types ... Setting up python3-sympy (1.13.3-2) ... Setting up python3.12-tk (3.12.9-1) ... Setting up libgomp1:amd64 (14.2.0-16) ... Setting up python3.13-tk (3.13.2-1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Feb 6 21:57:41 UTC 2025. Universal Time is now: Thu Feb 6 21:57:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Setting up libatomic1:amd64 (14.2.0-16) ... Setting up cython3 (3.0.11+dfsg-1+b1) ... Setting up libsepol2:amd64 (3.8-1) ... Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up python3-numpy (1:2.2.2+ds-2) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up mount (2.40.4-3) ... Setting up libopenjp2-7:amd64 (2.5.3-1) ... Setting up python3.13-minimal (3.13.2-1) ... Setting up mawk (1.3.4.20250131-1) ... Setting up python3-biopython (1.85+dfsg-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up login (1:4.16.0-2+really2.40.4-3) ... Setting up python3.13 (3.13.2-1) ... Setting up python3-pomegranate (0.15.0-1) ... Setting up cnvkit (0.9.12-1) ... Setting up python3-pil:amd64 (11.1.0-5) ... Setting up libglib2.0-0t64:amd64 (2.83.3-2) ... No schema files found: doing nothing. Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... Processing triggers for libc-bin (2.40-6) ... 1m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-yf', 'dist-upgrade'] 1m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m7.2s DUMP: 16ee04b16bbf80ffddfb15f4ec2a3e53 - 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 1m7.3s DUMP: Package: cnvkit Version: 0.9.12-1 Installed-Size: 94677 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate (>= 0.15), python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description-en: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Homepage: https://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.12-1_all.deb Size: 19867944 MD5sum: 1bab2eed9e247c45124199c37a680e14 SHA256: ae91c2bce847494e0e295aad3888522f2575eef877bd24355d13ac8236ceac8a 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 1m7.3s INFO: apt-cache knows about the following packages: cnvkit 1m7.3s INFO: Running scripts pre_install 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_database-server'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_database-server'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_exceptions'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_exceptions'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_extras'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_extras'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy'] 1m7.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy', 'cnvkit'] 1m7.4s DUMP: cnvkit: Installed: 0.9.12-1 Candidate: 0.9.12-1 Version table: *** 0.9.12-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy', 'cnvkit'] 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-y', 'install', 'cnvkit'] 1m7.6s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.12-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-y', 'install', 'cnvkit'] 1m7.6s INFO: Running scripts post_install 1m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_install_exceptions'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_install_exceptions'] 1m7.7s INFO: Running scripts post_distupgrade 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_exceptions'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_exceptions'] 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_zz_backports'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_distupgrade_zz_backports'] 1m7.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m8.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m8.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m9.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m9.6s INFO: Running scripts pre_install 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_database-server'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_database-server'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_exceptions'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_exceptions'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_extras'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_extras'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy'] 1m9.6s 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: 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy', 'cnvkit'] 1m9.6s DUMP: cnvkit: Installed: 0.9.12-1 Candidate: 0.9.12-1 Version table: *** 0.9.12-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-cache', 'policy', 'cnvkit'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-y', 'install', 'cnvkit=0.9.12-1'] 1m9.9s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.12-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', '-y', 'install', 'cnvkit=0.9.12-1'] 1m9.9s INFO: Running scripts post_install 1m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_install_exceptions'] 1m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_install_exceptions'] 1m9.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m11.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', '-ac', '--ignore-obsolete'] 1m14.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', '-ac', '--ignore-obsolete'] 1m14.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m14.2s DUMP: 0.15.6 1m14.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m14.2s INFO: Running adequate version 0.15.6 now. 1m14.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'cnvkit'] 1m14.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'cnvkit'] 1m14.2s INFO: Running scripts pre_remove 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_exceptions'] 1m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/pre_remove_exceptions'] 1m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m16.1s DUMP: install ok installed apt apt 2.9.27 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.4-3 install ok installed ca-certificates ca-certificates 20241223 install ok installed cnvkit cnvkit 0.9.12-1 install ok installed coreutils coreutils 9.5-1+b1 install ok installed cython3 cython3 3.0.11+dfsg-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-2 install ok installed fontconfig-config fontconfig-config 2.15.0-2 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-lyx fonts-lyx 2.4.3-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-16 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.27 install ok installed libatomic1:amd64 libatomic1 14.2.0-16 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.40.4-3 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-6 install ok installed libc6:amd64 libc6 2.40-6 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.11.1-1+b1 install ok installed libcurl4t64:amd64 libcurl4t64 8.11.1-1+b1 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 0.277 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-16 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.83.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-16 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-4 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu72:amd64 libicu72 72.1-6 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-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 1.21.3-4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-4 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-4 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 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 libldap2:amd64 libldap2 2.6.9+dfsg-1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 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 2.40.4-3 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250125-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.6.0-2 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.9.1-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.9.1-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-2 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-2 install ok installed libpam-runtime libpam-runtime 1.7.0-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-2 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.56.1-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.56.1-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.56.1-1 install ok installed libpaper-utils libpaper-utils 2.2.5-0.3 install ok installed libpaper2:amd64 libpaper2 2.2.5-0.3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.46-4 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.1-2 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.2-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.2-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 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+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.8-1 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 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+20250125-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-3 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b4 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+b3 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-3 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 11.0.0 install ok installed mount mount 2.40.4-3 install ok installed ncurses-base ncurses-base 6.5+20250125-2 install ok installed ncurses-bin ncurses-bin 6.5+20250125-2 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.4.0-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed procps procps 2:4.0.4-7 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.13.1-2 install ok installed python3-attr python3-attr 24.3.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.85+dfsg-2 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 install ok installed python3-cairo python3-cairo 1.26.1-2+b1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-contourpy python3-contourpy 1.3.1-1 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-decorator python3-decorator 5.1.1-5 install ok installed python3-fonttools python3-fonttools 4.55.3-2 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-6 install ok installed python3-importlib-metadata python3-importlib-metadata 8.6.1-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-joblib python3-joblib 1.3.2-6 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1+b1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-1 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3+b3 install ok installed python3-minimal python3-minimal 3.13.1-2 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-networkx python3-networkx 3.2.1-5 install ok installed python3-numpy python3-numpy 1:2.2.2+ds-2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.2+ds-2 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pandas python3-pandas 2.2.3+dfsg-7 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-7 install ok installed python3-pil:amd64 python3-pil 11.1.0-5 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-5 install ok installed python3-pkg-resources python3-pkg-resources 75.6.0-1 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-pomegranate python3-pomegranate 0.15.0-1 install ok installed python3-pyfaidx python3-pyfaidx 0.8.1.3-1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b2 install ok installed python3-reportlab python3-reportlab 4.2.5-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.14.1-4 install ok installed python3-sklearn python3-sklearn 1.4.2+dfsg-7 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 1.4.2+dfsg-7+b1 install ok installed python3-sympy python3-sympy 1.13.3-2 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.13.1-1 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 2024.2-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3-yaml python3-yaml 6.0.2-1+b1 install ok installed python3-zipp python3-zipp 3.21.0-1 install ok installed python3.12-tk python3.12-tk 3.12.9-1 install ok installed python3.13 python3.13 3.13.2-1 install ok installed python3.13-minimal python3.13-minimal 3.13.2-1 install ok installed python3.13-tk python3.13-tk 3.13.2-1 install ok installed r-base-core r-base-core 4.4.2-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.52.0-2 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.80.0-2 install ok installed readline-common readline-common 8.2-6 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 sqv sqv 1.2.1-6 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2025a-2 install ok installed ucf ucf 3.0049 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+nmu2 install ok installed util-linux util-linux 2.40.4-3 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xdg-utils xdg-utils 1.2.1-2 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 1m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'remove', 'blt', 'ca-certificates', 'cython3', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-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', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libunistring5: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', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip', 'cnvkit'] 1m36.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt ca-certificates cnvkit cython3 fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libunistring5 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 media-types netbase openssl procps python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-yaml python3-zipp python3.12-tk python3.13 python3.13-minimal python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common sensible-utils sgml-base 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, 191 to remove and 0 not upgraded. After this operation, 951 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 ... 25823 files and directories currently installed.) Removing cnvkit (0.9.12-1) ... Removing python3-biopython (1.85+dfsg-2) ... Removing python3-reportlab (4.2.5-1) ... Removing python3-matplotlib (3.8.3-3+b3) ... Removing python3-pil.imagetk:amd64 (11.1.0-5) ... Removing python3-pil:amd64 (11.1.0-5) ... Removing python3-tk:amd64 (3.13.1-1) ... Removing blt (2.5.3+dfsg-7) ... Removing r-bioc-dnacopy (1.80.0-2) ... Removing r-bioc-biocgenerics (0.52.0-2) ... Removing r-base-core (4.4.2-1) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-pomegranate (0.15.0-1) ... Removing cython3 (3.0.11+dfsg-1+b1) ... Removing libpangocairo-1.0-0:amd64 (1.56.1-1) ... Removing libpangoft2-1.0-0:amd64 (1.56.1-1) ... Removing libpango-1.0-0:amd64 (1.56.1-1) ... Removing fontconfig (2.15.0-2) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.2-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2+b1) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.3-1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1) ... Removing libglib2.0-0t64:amd64 (2.83.3-2) ... Removing libatomic1:amd64 (14.2.0-16) ... Removing python3-sklearn (1.4.2+dfsg-7) ... Removing python3-sklearn-lib:amd64 (1.4.2+dfsg-7+b1) ... Removing python3-pandas (2.2.3+dfsg-7) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-7) ... Removing python3-contourpy (1.3.1-1) ... Removing python3-freetype (2.5.1-1) ... Removing libcurl4t64:amd64 (8.11.1-1+b1) ... Removing python3-pysam (0.22.1+ds-2+b2) ... Removing libhts3t64:amd64 (1.20+ds-2) ... Removing libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... 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 (1.23-1+b1) ... Removing python3-yaml (6.0.2-1+b1) ... Removing python3-networkx (3.2.1-5) ... Removing python3-pkg-resources (75.6.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-16) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-4) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Removing libsm6:amd64 (2:1.2.4-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libkrb5-3:amd64 (1.21.3-4) ... Removing libk5crypto3:amd64 (1.21.3-4) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-4) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.9+dfsg-1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing ucf (3.0049) ... Removing python3-joblib (1.3.2-6) ... Removing procps (2:4.0.4-7) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.6.0-2) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Removing libngtcp2-16:amd64 (1.9.1-1) ... Removing libopenjp2-7:amd64 (2.5.3-1) ... Removing libpaper-utils (2.2.5-0.3) ... Removing libpaper2:amd64 (2.2.5-0.3) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libproc2-0:amd64 (2:4.0.4-7) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Removing libwebpmux3:amd64 (1.5.0-0.1) ... Removing libwebpdemux2:amd64 (1.5.0-0.1) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing python3.12-tk (3.12.9-1) ... Removing libtext-wrapi18n-perl (0.06-10) ... Removing libtext-charwidth-perl:amd64 (0.04-11+b4) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libyaml-0-2:amd64 (0.2.5-2) ... Removing openssl (3.4.0-2) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-pyfaidx (0.8.1.3-1) ... Removing python3-importlib-metadata (8.6.1-1) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-kiwisolver (1.4.7-3) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-packaging (24.2-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3-zipp (3.21.0-1) ... Removing sensible-utils (0.0.24) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing unzip (6.0-28) ... Removing xdg-utils (1.2.1-2) ... Removing zip (3.0-14) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing libfontconfig1:amd64 (2.15.0-2) ... Removing fontconfig-config (2.15.0-2) ... Removing fonts-urw-base35 (20200910-8) ... Removing xfonts-utils (1:7.7+7) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libgnutls30t64:amd64 (3.8.8-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libidn2-0:amd64 (2.3.7-2+b1) ... Removing libpng16-16t64:amd64 (1.6.46-4) ... Removing libtasn1-6:amd64 (4.19.0-3+b3) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libunistring5:amd64 (1.3-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b4) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing python3-fonttools (4.55.3-2) ... Removing python3-scipy (1.14.1-4) ... Removing python3-numpy (1:2.2.2+ds-2) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-sympy (1.13.3-2) ... Removing python3-lxml:amd64 (5.3.0-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing libgcrypt20:amd64 (1.11.0-7) ... Removing libgfortran5:amd64 (14.2.0-16) ... Removing libgpg-error0:amd64 (1.51-3) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-6) ... Removing python3-brotli (1.1.0-2+b6) ... Removing python3-decorator (5.1.1-5) ... Removing python3-fs (2.4.16-6) ... Removing python3-lz4 (4.4.0+dfsg-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-tz (2024.2-1) ... Removing unicode-data (15.1.0-1) ... Removing python3-ufolib2 (0.17.0+dfsg1-1) ... Removing python3-attr (24.3.0-1) ... Removing python3 (3.13.1-2) ... Removing python3.13 (3.13.2-1) ... Removing python3-minimal (3.13.1-2) ... Removing python3.13-minimal (3.13.2-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.13.1-2) ... Removing libpython3.13-stdlib:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.6-1) ... Removing libncursesw6:amd64 (6.5+20250125-2) ... Removing libpython3.13-minimal:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... 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 media-types (11.0.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-6) ... 1m36.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'remove', 'blt', 'ca-certificates', 'cython3', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-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', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libunistring5: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', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip', 'cnvkit'] 1m36.8s INFO: Running scripts post_remove 1m36.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_remove_exceptions'] 1m36.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_remove_exceptions'] 1m36.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--purge', 'blt', 'ca-certificates', 'cython3', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-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', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libunistring5: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', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip'] 1m37.2s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5100 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cython3 which isn't installed Purging configuration files for fontconfig (2.15.0-2) ... Purging configuration files for fontconfig-config (2.15.0-2) ... 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-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove 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 libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 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 libgcrypt20 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.83.3-2) ... dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpg-error0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-4) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 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 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 libldap2 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 libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 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 libpaper2:amd64 (2.2.5-0.3) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.2-1) ... dpkg: warning: ignoring request to remove libpython3.13-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 (8.2-6) ... 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 libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtext-charwidth-perl which isn't installed dpkg: warning: ignoring request to remove libtext-wrapi18n-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed 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 libunistring5 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 Purging configuration files for media-types (11.0.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.4.0-2) ... Purging configuration files for procps (2:4.0.4-7) ... Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.13.1-2) ... 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-chardet 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-decorator 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-importlib-metadata 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-joblib 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-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-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib 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-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-pomegranate which isn't installed dpkg: warning: ignoring request to remove python3-pyfaidx which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-sklearn which isn't installed dpkg: warning: ignoring request to remove python3-sklearn-lib which isn't installed Purging configuration files for python3-sympy (1.13.3-2) ... dpkg: warning: ignoring request to remove python3-threadpoolctl which isn't installed dpkg: warning: ignoring request to remove python3-tk 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-yaml which isn't installed dpkg: warning: ignoring request to remove python3-zipp which isn't installed dpkg: warning: ignoring request to remove python3.12-tk which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.2-1) ... 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-dnacopy which isn't installed Purging configuration files for readline-common (8.2-6) ... 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 tk8.6-blt2.5 which isn't installed Purging configuration files for ucf (3.0049) ... 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+24) ... 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 1m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--purge', 'blt', 'ca-certificates', 'cython3', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-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', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libunistring5: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', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ucf', 'unicode-data', 'unzip', 'w3c-sgml-lib', 'x11-common', 'xdg-utils', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zip'] 1m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--purge', 'cnvkit'] 1m37.2s DUMP: dpkg: warning: ignoring request to remove cnvkit which isn't installed 1m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--purge', 'cnvkit'] 1m37.2s INFO: Running scripts post_purge 1m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_purge_exceptions'] 1m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_purge_exceptions'] 1m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--purge', '--pending'] 1m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--purge', '--pending'] 1m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--remove', '--pending'] 1m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg', '--remove', '--pending'] 1m37.2s INFO: Running scripts post_test 1m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_test_exceptions'] 1m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'tmp/scripts/post_test_exceptions'] 1m37.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m37.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg-divert', '--list'] 1m37.4s 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 1m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'dpkg-divert', '--list'] 1m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'clean'] 1m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpczag7hcq', 'apt-get', 'clean'] 1m37.4s DEBUG: Recording chroot state 1m37.7s 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 1m37.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/shm'] 1m37.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/shm'] 1m37.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/console'] 1m37.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/console'] 1m37.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/ptmx'] 1m37.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/ptmx'] 1m37.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/pts'] 1m37.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/dev/pts'] 1m37.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/proc'] 1m38.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpczag7hcq/proc'] 1m38.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m38.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpczag7hcq'] 1m38.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpczag7hcq 1m38.1s INFO: PASS: Upgrading between Debian distributions. 1m38.1s INFO: PASS: All tests. 1m38.1s INFO: piuparts run ends. ret=0 End: 2025-02-06 21:58:16 GMT