Start: 2024-07-22 21:09:39 GMT [sid] 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 [experimental] Package: cnvkit Version: 0.9.10-3~0exp0 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 (>= 1.78.0) 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_0.9.10-3~0exp0_all.deb Size: 19505196 MD5sum: 81a8ff12505ee9ec71a6417c8ee47beb SHA256: 776e6a92838839190a1d5826149fcf1f8da4187a20c6b26f83d7c65a4564192d 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/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt 'cnvkit=0.9.10-3~0exp0' 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 1.4.2 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/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt 'cnvkit=0.9.10-3~0exp0' 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-31-amd64 #1 SMP Debian 5.10.221-1 (2024-07-14) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpzeuej9cy 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpzeuej9cy 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/ptmx'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/ptmx'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpzeuej9cy/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'update'] 0m4.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9981 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7249 kB] Fetched 17.4 MB in 3s (5709 kB/s) Reading package lists... 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'update'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-yf', 'dist-upgrade'] 0m6.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: dpkg login passwd 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3067 kB of archives. After this operation, 4096 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.8 [1529 kB] Get:2 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.15.3-3 [564 kB] Get:3 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.15.3-3 [974 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3067 kB in 0s (43.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5175 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.22.8_amd64.deb ... Unpacking dpkg (1.22.8) over (1.22.7) ... Setting up dpkg (1.22.8) ... (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 ... 5175 files and directories currently installed.) Preparing to unpack .../login_1%3a4.15.3-3_amd64.deb ... Unpacking login (1:4.15.3-3) over (1:4.15.3-2) ... Preparing to unpack .../passwd_1%3a4.15.3-3_amd64.deb ... Unpacking passwd (1:4.15.3-3) over (1:4.15.3-2) ... Setting up login (1:4.15.3-3) ... Setting up passwd (1:4.15.3-3) ... 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-yf', 'dist-upgrade'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s DUMP: 98acebfd84b3487629e014a4c8b5582b - 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s INFO: Running scripts post_setup 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_dummy_users'] 0m8.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_dummy_users'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_forbid_home'] 0m8.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_forbid_home'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_minimize'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_minimize'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_zz_backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_setup_zz_backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.2s DUMP: install ok installed apt apt 2.9.6 install ok installed base-files base-files 13.3 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.21-2.1 install ok installed bsdutils bsdutils 1:2.40.2-1 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.8 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14.1.0-5 install ok installed gpgv gpgv 2.2.43-7 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.6 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.39-4 install ok installed libc6:amd64 libc6 2.39-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.1.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.49-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b3 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsepol2:amd64 libsepol2 3.5-2+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.2.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.1.0-5 install ok installed libsystemd0:amd64 libsystemd0 256.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.2-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.15.3-3 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240622-2 install ok installed mount mount 2.40.2-1 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed passwd passwd 1:4.15.3-3 install ok installed perl-base perl-base 5.38.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.09-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 0m8.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 0m8.6s INFO: Running scripts is_testable 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/is_testable_uninstallable'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/is_testable_uninstallable'] 0m8.6s INFO: Running scripts pre_test 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_test_exceptions'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_test_exceptions'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_test_root_password'] 0m8.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_test_root_password'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m8.9s 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 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m8.9s INFO: apt-cache knows about the following packages: cnvkit 0m8.9s INFO: Running scripts pre_install 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_database-server'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_database-server'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_extras'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_extras'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy'] 0m9.0s 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: 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy', 'cnvkit'] 0m9.1s DUMP: cnvkit: Installed: (none) Candidate: 0.9.10-2 Version table: 0.9.10-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy', 'cnvkit'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-y', 'install', 'cnvkit'] 2m14.7s 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 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-0-2 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr 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-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-yaml python3-zipp python3.12 python3.12-minimal 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 low-memory-monitor 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-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 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 python3.12-venv python3.12-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit readline-doc sgml-base-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules psmisc linux-sysctl-defaults python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson 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 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 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-0-2 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr 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-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-yaml python3-zipp python3.12 python3.12-minimal 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, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 189 MB of archives. After this operation, 767 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.4-3 [812 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:3 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.4-3 [2137 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.4-1 [26.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Get:8 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.0-1 [902 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.4-3 [1950 kB] Get:12 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.4-3 [664 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.4-1 [9500 B] Get:14 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.4-1 [27.6 kB] Get:15 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get:17 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get:18 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.2.2-1 [1364 kB] Get:20 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:21 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:26 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:27 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:29 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:30 http://deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:31 http://deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:32 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:33 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:45 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:46 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:47 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.1.0-5 [836 kB] Get:49 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:50 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 70.3.0-2 [264 kB] Get:51 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-10+b1 [4212 kB] Get:52 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:53 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.12.4-2 [109 kB] Get:54 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.4.0-1 [79.4 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.1.0-5 [137 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:58 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.80.4-1 [1486 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:67 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get:73 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:78 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.26.1-1+b1 [114 kB] Get:79 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-2 [78.6 kB] Get:80 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:81 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.2.2-1 [1150 kB] Get:82 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:83 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:84 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.83+dfsg1-3+b1 [1606 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:87 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.1-2 [189 kB] Get:88 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get:89 http://deb.debian.org/debian sid/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get:90 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get:91 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:92 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.0.7-3+b1 [194 kB] Get:93 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:94 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b4 [309 kB] Get:95 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:96 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:97 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.12.0-2+b1 [16.4 MB] Get:98 http://deb.debian.org/debian sid/main amd64 python3-zipp all 3.19.2-2 [10.2 kB] Get:99 http://deb.debian.org/debian sid/main amd64 python3-importlib-metadata all 8.0.0-2 [19.5 kB] Get:100 http://deb.debian.org/debian sid/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:101 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:103 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.12.1-1 [3869 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:106 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1.1 [232 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.2.2-1 [1208 kB] Get:111 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b4 [25.2 kB] Get:112 http://deb.debian.org/debian sid/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b2 [298 kB] Get:113 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:114 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.46.0-1+b1 [1382 kB] Get:115 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.5-1+b1 [59.5 kB] Get:116 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get:118 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.6.3-2+b1 [6923 kB] Get:119 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.2.2+dfsg-4+b1 [4115 kB] Get:120 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get:121 http://deb.debian.org/debian sid/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get:122 http://deb.debian.org/debian sid/main amd64 python3-networkx all 3.2.1-4 [14.2 MB] Get:123 http://deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:124 http://deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0.1-2+b1 [120 kB] Get:125 http://deb.debian.org/debian sid/main amd64 python3-pomegranate amd64 0.14.8-6+b1 [2557 kB] Get:126 http://deb.debian.org/debian sid/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:130 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-2 [186 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.3.0-2 [64.7 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.5.0-2 [126 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.5.0-2 [22.9 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:140 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.8.0-4 [451 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:145 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get:146 http://deb.debian.org/debian sid/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:147 http://deb.debian.org/debian sid/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-3+b1 [3497 kB] Get:148 http://deb.debian.org/debian sid/main amd64 python3-sklearn all 1.4.2+dfsg-3 [2247 kB] Get:149 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-13 [230 kB] Get:150 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:153 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.8.0-4 [445 kB] Get:155 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [219 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [48.0 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [35.0 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:167 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.1-1 [28.3 MB] Get:168 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:169 http://deb.debian.org/debian sid/main amd64 r-bioc-dnacopy amd64 1.76.0-1 [380 kB] Get:170 http://deb.debian.org/debian sid/main amd64 cnvkit all 0.9.10-2 [19.5 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 189 MB in 7s (25.4 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5179 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.4-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.4-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.4-3_amd64.deb ... Unpacking python3.12-minimal (3.12.4-3) ... Setting up libpython3.12-minimal:amd64 (3.12.4-3) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.4-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5499 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.4-1_amd64.deb ... Unpacking python3-minimal (3.12.4-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.5-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.46.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.0-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../7-libpython3.12-stdlib_3.12.4-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.4-3) ... Selecting previously unselected package python3.12. 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Preparing to unpack .../000-python3_3.12.4-1_amd64.deb ... Unpacking python3 (3.12.4-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-5_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-5_amd64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.2.2-1_amd64.deb ... Unpacking openssl (3.2.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../008-libtcl8.6_8.6.14+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../009-libbrotli1_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../010-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../011-libfreetype6_2.13.2+dfsg-1+b4_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../012-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../013-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../014-libfontenc1_1%3a1.1.8-1_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../015-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../016-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../017-xfonts-utils_1%3a7.7+6_amd64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../018-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../019-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../020-libfontconfig1_2.15.0-1.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../021-libxau6_1%3a1.0.9-1+b1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../022-libxdmcp6_1%3a1.1.2-3+b1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../023-libxcb1_1.17.0-2_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../024-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../025-libx11-6_2%3a1.8.7-1+b1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../026-libxrender1_1%3a0.9.10-1.1+b1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../027-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../028-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../029-libxss1_1%3a1.2.3-1+b1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../030-libtk8.6_8.6.14-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.14-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../031-tk8.6-blt2.5_2.5.3+dfsg-7_amd64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... Selecting previously unselected package blt. Preparing to unpack .../032-blt_2.5.3+dfsg-7_amd64.deb ... Unpacking blt (2.5.3+dfsg-7) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../033-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../034-libgfortran5_14.1.0-5_amd64.deb ... Unpacking libgfortran5:amd64 (14.1.0-5) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../035-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../036-python3-pkg-resources_70.3.0-2_all.deb ... 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Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../140-libcurl4t64_8.8.0-4_amd64.deb ... Unpacking libcurl4t64:amd64 (8.8.0-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../141-fontconfig_2.15.0-1.1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../142-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../143-libdatrie1_0.2.13-3_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-3) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../144-libthai0_0.1.29-2_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-2) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../145-libpango-1.0-0_1.54.0+ds-1_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.54.0+ds-1) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../146-libpangoft2-1.0-0_1.54.0+ds-1_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../147-libpangocairo-1.0-0_1.54.0+ds-1_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../148-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../149-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../150-libice6_2%3a1.0.10-1+b1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1+b1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../151-libsm6_2%3a1.2.3-1+b1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1+b1) ... Selecting previously unselected package libxt6t64:amd64. Preparing to unpack .../152-libxt6t64_1%3a1.2.1-1.2_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2) ... Selecting previously unselected package r-base-core. Preparing to unpack .../153-r-base-core_4.4.1-1_amd64.deb ... Unpacking r-base-core (4.4.1-1) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../154-r-bioc-biocgenerics_0.48.1-2_all.deb ... Unpacking r-bioc-biocgenerics (0.48.1-2) ... Selecting previously unselected package r-bioc-dnacopy. Preparing to unpack .../155-r-bioc-dnacopy_1.76.0-1_amd64.deb ... Unpacking r-bioc-dnacopy (1.76.0-1) ... Selecting previously unselected package cnvkit. Preparing to unpack .../156-cnvkit_0.9.10-2_all.deb ... Unpacking cnvkit (0.9.10-2) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.1-2) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libsqlite3-0:amd64 (3.46.0-1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libgomp1:amd64 (14.1.0-5) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up unicode-data (15.1.0-1) ... Setting up zip (3.0-13) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up libglib2.0-0t64:amd64 (2.80.4-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14.1.0-5) ... Setting up libnghttp3-9:amd64 (1.3.0-2) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up procps (2:4.0.4-5) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.5.0-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up openssl (3.2.2-1) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libngtcp2-crypto-gnutls8:amd64 (1.5.0-2) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-2) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.4-3) ... Setting up libcurl4t64:amd64 (8.8.0-4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up python3.12 (3.12.4-3) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libcurl3t64-gnutls:amd64 (8.8.0-4) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libpython3-stdlib:amd64 (3.12.4-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3 (3.12.4-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-zipp (3.19.2-2) ... Setting up python3-freetype (2.4.0-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.4.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b4) ... Setting up python3-cycler (0.12.1-1) ... Setting up r-base-core (4.4.1-1) ... Creating config file /etc/R/Renviron with new version Setting up python3-kiwisolver (1.4.5-1+b1) ... Setting up python3-lxml:amd64 (5.2.2-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-sympy (1.12.1-1) ... Setting up python3-attr (23.2.0-2) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-cairo (1.26.1-1+b1) ... Setting up python3-importlib-metadata (8.0.0-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b4) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b2) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-yaml (6.0.1-2+b1) ... Setting up python3-tk:amd64 (3.12.4-2) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-10+b1) ... Setting up python3-reportlab (4.2.2-1) ... Setting up r-bioc-dnacopy (1.76.0-1) ... Setting up python3-contourpy (1.0.7-3+b1) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up python3-scipy (1.12.0-2+b1) ... Setting up python3-pomegranate (0.14.8-6+b1) ... Setting up python3-pandas-lib:amd64 (2.2.2+dfsg-4+b1) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-3+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up python3-sklearn (1.4.2+dfsg-3) ... Setting up python3-fonttools (4.46.0-1+b1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2+b1) ... Processing triggers for libc-bin (2.39-4) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-3+b1) ... Setting up cnvkit (0.9.10-2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 2m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-y', 'install', 'cnvkit'] 2m14.7s INFO: Running scripts post_install 2m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_install_exceptions'] 2m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_install_exceptions'] 2m14.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m15.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m15.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpzeuej9cy to experimental 2m15.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 2m15.8s INFO: Running scripts pre_distupgrade 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_exceptions'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_exceptions'] 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'update'] 2m17.8s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Get:2 http://deb.debian.org/debian experimental InRelease [101 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 Packages [618 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [352 kB] Fetched 1071 kB in 1s (1235 kB/s) Reading package lists... 2m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'update'] 2m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-yf', 'dist-upgrade'] 2m18.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-yf', 'dist-upgrade'] 2m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m18.9s DUMP: b86851f1aed9a5022e62e785cce2b426 - 2m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 2m19.3s 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 2m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 2m19.3s INFO: apt-cache knows about the following packages: cnvkit 2m19.3s INFO: Running scripts pre_install 2m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_database-server'] 2m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_database-server'] 2m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_exceptions'] 2m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_exceptions'] 2m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_extras'] 2m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_extras'] 2m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture'] 2m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture'] 2m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy'] 2m19.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 2m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy'] 2m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy', 'cnvkit'] 2m19.4s DUMP: cnvkit: Installed: 0.9.10-2 Candidate: 0.9.10-2 Version table: 0.9.10-3~0exp0 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 0.9.10-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy', 'cnvkit'] 2m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-y', '-t', 'experimental', 'install', 'cnvkit'] 2m24.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: r-bioc-biocgenerics r-bioc-dnacopy The following packages will be upgraded: cnvkit r-bioc-biocgenerics r-bioc-dnacopy 3 upgraded, 0 newly installed, 0 to remove and 18 not upgraded. Need to get 20.5 MB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://deb.debian.org/debian experimental/main amd64 r-bioc-dnacopy amd64 1.78.0-1~0exp [378 kB] Get:2 http://deb.debian.org/debian experimental/main amd64 r-bioc-biocgenerics all 0.50.0-1~0exp [606 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 cnvkit all 0.9.10-3~0exp0 [19.5 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.5 MB in 2s (11.7 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 ... 24616 files and directories currently installed.) Preparing to unpack .../r-bioc-dnacopy_1.78.0-1~0exp_amd64.deb ... Unpacking r-bioc-dnacopy (1.78.0-1~0exp) over (1.76.0-1) ... Preparing to unpack .../r-bioc-biocgenerics_0.50.0-1~0exp_all.deb ... Unpacking r-bioc-biocgenerics (0.50.0-1~0exp) over (0.48.1-2) ... Preparing to unpack .../cnvkit_0.9.10-3~0exp0_all.deb ... Unpacking cnvkit (0.9.10-3~0exp0) over (0.9.10-2) ... Setting up r-bioc-biocgenerics (0.50.0-1~0exp) ... Setting up r-bioc-dnacopy (1.78.0-1~0exp) ... Setting up cnvkit (0.9.10-3~0exp0) ... 2m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-y', '-t', 'experimental', 'install', 'cnvkit'] 2m24.0s INFO: Running scripts post_install 2m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_install_exceptions'] 2m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_install_exceptions'] 2m24.0s INFO: Running scripts post_distupgrade 2m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_exceptions'] 2m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_exceptions'] 2m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_zz_backports'] 2m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_distupgrade_zz_backports'] 2m24.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m25.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m25.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m26.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m26.3s INFO: Running scripts pre_install 2m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_database-server'] 2m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_database-server'] 2m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_exceptions'] 2m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_exceptions'] 2m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_extras'] 2m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_extras'] 2m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture'] 2m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture'] 2m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy'] 2m26.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 2m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy'] 2m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy', 'cnvkit'] 2m26.5s DUMP: cnvkit: Installed: 0.9.10-3~0exp0 Candidate: 0.9.10-3~0exp0 Version table: *** 0.9.10-3~0exp0 100 1 http://deb.debian.org/debian experimental/main amd64 Packages 100 /var/lib/dpkg/status 0.9.10-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 2m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-cache', 'policy', 'cnvkit'] 2m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-y', '-t', 'experimental', 'install', 'cnvkit=0.9.10-3~0exp0'] 2m27.3s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.10-3~0exp0). 0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded. 2m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', '-y', '-t', 'experimental', 'install', 'cnvkit=0.9.10-3~0exp0'] 2m27.3s INFO: Running scripts post_install 2m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_install_exceptions'] 2m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_install_exceptions'] 2m27.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m28.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 2m30.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', '-ac', '--ignore-obsolete'] 2m34.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', '-ac', '--ignore-obsolete'] 2m34.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m34.5s DUMP: 0.15.6 2m34.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m34.5s INFO: Running adequate version 0.15.6 now. 2m34.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'cnvkit'] 2m34.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'cnvkit'] 2m34.8s INFO: Running scripts pre_remove 2m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_exceptions'] 2m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/pre_remove_exceptions'] 2m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m40.0s DUMP: install ok installed apt apt 2.9.6 install ok installed base-files base-files 13.3 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.21-2.1 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-1 install ok installed ca-certificates ca-certificates 20240203 install ok installed cnvkit cnvkit 0.9.10-3~0exp0 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.8 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-2 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.1-2 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.1.0-5 install ok installed gpgv gpgv 2.2.43-7 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.6 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.39-4 install ok installed libc6:amd64 libc6 2.39-4 install ok installed libcairo2:amd64 libcairo2 1.18.0-3+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.8.0-4 install ok installed libcurl4t64:amd64 libcurl4t64 8.8.0-4 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b4 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14.1.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-2 install ok installed libgfortran5:amd64 libgfortran5 14.1.0-5 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.80.4-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgomp1:amd64 libgomp1 14.1.0-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.49-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libice6:amd64 libice6 2:1.0.10-1+b1 install ok installed libicu72:amd64 libicu72 72.1-5 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.62.1-2 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.3.0-2 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.5.0-2 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.5.0-2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29+b1 install ok installed libpaper1:amd64 libpaper1 1.1.29+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-5 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.4-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.4-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.4-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b1 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b3 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsepol2:amd64 libsepol2 3.5-2+b1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.0-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-5 install ok installed libssl3t64:amd64 libssl3t64 3.2.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.1.0-5 install ok installed libsystemd0:amd64 libsystemd0 256.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libudev1:amd64 libudev1 256.2-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-1 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1+b1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1+b1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2 install ok installed libxcb1:amd64 libxcb1 1.17.0-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg-3+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.15.3-3 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240622-2 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-1 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.2.2-1 install ok installed passwd passwd 1:4.15.3-3 install ok installed perl-base perl-base 5.38.2-5 install ok installed procps procps 2:4.0.4-5 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-2 install ok installed python3 python3 3.12.4-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 23.2.0-2 install ok installed python3-biopython python3-biopython 1.83+dfsg1-3+b1 install ok installed python3-brotli python3-brotli 1.1.0-2+b4 install ok installed python3-cairo python3-cairo 1.26.1-1+b1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-contourpy python3-contourpy 1.0.7-3+b1 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-2 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-fonttools python3-fonttools 4.46.0-1+b1 install ok installed python3-freetype python3-freetype 2.4.0-2 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-importlib-metadata python3-importlib-metadata 8.0.0-2 install ok installed python3-joblib python3-joblib 1.3.2-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.5-1+b1 install ok installed python3-lxml:amd64 python3-lxml 5.2.2-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b4 install ok installed python3-matplotlib python3-matplotlib 3.6.3-2+b1 install ok installed python3-minimal python3-minimal 3.12.4-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-networkx python3-networkx 3.2.1-4 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-10+b1 install ok installed python3-packaging python3-packaging 24.1-1 install ok installed python3-pandas python3-pandas 2.2.2+dfsg-4 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.2+dfsg-4+b1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.4.0-1 install ok installed python3-pkg-resources python3-pkg-resources 70.3.0-2 install ok installed python3-pomegranate python3-pomegranate 0.14.8-6+b1 install ok installed python3-pyfaidx python3-pyfaidx 0.8.1.1-2 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b1 install ok installed python3-reportlab python3-reportlab 4.2.2-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.12.0-2+b1 install ok installed python3-six python3-six 1.16.0-6 install ok installed python3-sklearn python3-sklearn 1.4.2+dfsg-3 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 1.4.2+dfsg-3+b1 install ok installed python3-sympy python3-sympy 1.12.1-1 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.12.4-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b2 install ok installed python3-yaml python3-yaml 6.0.1-2+b1 install ok installed python3-zipp python3-zipp 3.19.2-2 install ok installed python3.12 python3.12 3.12.4-3 install ok installed python3.12-minimal python3.12-minimal 3.12.4-3 install ok installed r-base-core r-base-core 4.4.1-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.50.0-1~0exp install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.78.0-1~0exp install ok installed readline-common readline-common 8.2-4 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 sysvinit-utils sysvinit-utils 3.09-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024a-4 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.19 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 2m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72: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', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', '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-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12', 'python3.12-minimal', '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'] 3m43.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt ca-certificates cnvkit fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-0-2 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr 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-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-yaml python3-zipp python3.12 python3.12-minimal 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, 170 to remove and 0 not upgraded. After this operation, 767 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 ... 24616 files and directories currently installed.) Removing cnvkit (0.9.10-3~0exp0) ... Removing python3-matplotlib (3.6.3-2+b1) ... Removing python3-biopython (1.83+dfsg1-3+b1) ... Removing python3-reportlab (4.2.2-1) ... Removing python3-pil.imagetk:amd64 (10.4.0-1) ... Removing python3-tk:amd64 (3.12.4-2) ... Removing blt (2.5.3+dfsg-7) ... Removing r-bioc-dnacopy (1.78.0-1~0exp) ... Removing r-bioc-biocgenerics (0.50.0-1~0exp) ... Removing r-base-core (4.4.1-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-1) ... Removing fontconfig (2.15.0-1.1) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-1+b1) ... Removing libcairo2:amd64 (1.18.0-3+b1) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing python-matplotlib-data (3.6.3-2) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.1-2) ... Removing fonts-urw-base35 (20200910-8) ... Removing python3-sklearn (1.4.2+dfsg-3) ... Removing python3-pomegranate (0.14.8-6+b1) ... Removing python3-sklearn-lib:amd64 (1.4.2+dfsg-3+b1) ... Removing python3-pandas (2.2.2+dfsg-4) ... Removing python3-pandas-lib:amd64 (2.2.2+dfsg-4+b1) ... Removing xfonts-utils (1:7.7+6) ... Removing libcurl4t64:amd64 (8.8.0-4) ... Removing python3-pysam (0.22.1+ds-2+b1) ... Removing libhts3t64:amd64 (1.20+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.8.0-4) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing python3-yaml (6.0.1-2+b1) ... Removing python3-pyfaidx (0.8.1.1-2) ... Removing python3-importlib-metadata (8.0.0-2) ... Removing python3-kiwisolver (1.4.5-1+b1) ... Removing libfontenc1:amd64 (1:1.1.8-1) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libsm6:amd64 (2:1.2.3-1+b1) ... Removing libice6:amd64 (2:1.0.10-1+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 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-2) ... Removing python3-joblib (1.3.2-2) ... Removing procps (2:4.0.4-5) ... Removing libnghttp2-14:amd64 (1.62.1-2) ... Removing libnghttp3-9:amd64 (1.3.0-2) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.5.0-2) ... Removing libngtcp2-16:amd64 (1.5.0-2) ... Removing libpaper-utils (1.1.29+b1) ... Removing libpaper1:amd64 (1.1.29+b1) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libproc2-0:amd64 (2:4.0.4-5) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libqhull-r8.0:amd64 (2020.2-6+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libssh2-1t64:amd64 (1.11.0-5) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libxss1:amd64 (1:1.2.3-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2) ... Removing libxcb-render0:amd64 (1.17.0-2) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libyaml-0-2:amd64 (0.2.5-1+b1) ... Removing openssl (3.2.2-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-contourpy (1.0.7-3+b1) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-2) ... Removing python3-freetype (2.4.0-2) ... Removing python3-networkx (3.2.1-4) ... Removing python3-packaging (24.1-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing python3-zipp (3.19.2-2) ... Removing ucf (3.0043+nmu1) ... 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 xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing python3-pil:amd64 (10.4.0-1) ... Removing libraqm0:amd64 (0.10.1-1+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libglib2.0-0t64:amd64 (2.80.4-1) ... Removing libimagequant0:amd64 (2.18.0-1+b1) ... Removing libgomp1:amd64 (14.1.0-5) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b3) ... Removing libwebpmux3:amd64 (1.4.0-0.1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1) ... Removing libwebp7:amd64 (1.4.0-0.1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1) ... Removing libx11-6:amd64 (2:1.8.7-1+b1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxcb1:amd64 (1.17.0-2) ... Removing libxau6:amd64 (1:1.0.9-1+b1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... Removing python3-attr (23.2.0-2) ... Removing python3-fonttools (4.46.0-1+b1) ... Removing python3-sympy (1.12.1-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-unicodedata2 (15.1.0+ds-1+b2) ... Removing python3-fs (2.4.16-4) ... Removing python3-six (1.16.0-6) ... Removing python3-lxml:amd64 (5.2.2-1) ... Removing libxslt1.1:amd64 (1.1.35-1.1) ... Removing libxml2:amd64 (2.12.7+dfsg-3+b1) ... Removing libicu72:amd64 (72.1-5) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-brotli (1.1.0-2+b4) ... Removing python3-lz4 (4.0.2+dfsg-1+b4) ... Removing python3-tz (2024.1-2) ... Removing unicode-data (15.1.0-1) ... Removing python3-scipy (1.12.0-2+b1) ... Removing python3-numpy (1:1.26.4+ds-10+b1) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libgfortran5:amd64 (14.1.0-5) ... Removing python3-decorator (5.1.1-5) ... Removing python3-pkg-resources (70.3.0-2) ... Removing python3 (3.12.4-1) ... Removing python3.12 (3.12.4-3) ... Removing python3-minimal (3.12.4-1) ... Removing python3.12-minimal (3.12.4-3) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpython3-stdlib:amd64 (3.12.4-1) ... Removing libpython3.12-stdlib:amd64 (3.12.4-3) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.5-2) ... Removing libpython3.12-minimal:amd64 (3.12.4-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-4) ... 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 (3.46.0-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-4) ... Processing triggers for libc-bin (2.39-4) ... 3m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72: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', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', '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-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12', 'python3.12-minimal', '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'] 3m43.2s INFO: Running scripts post_remove 3m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_remove_exceptions'] 3m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_remove_exceptions'] 3m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72: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', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', '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-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12', 'python3.12-minimal', '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'] 3m44.1s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5252 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed 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 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 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 libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.80.4-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29+b1) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.4-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.2.2-1) ... Purging configuration files for procps (2:4.0.4-5) ... Purging configuration files for python-matplotlib-data (3.6.3-2) ... Purging configuration files for python3 (3.12.4-1) ... dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-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-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-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-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-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-six 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 (1.12.1-1) ... 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-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 which isn't installed Purging configuration files for python3.12-minimal (3.12.4-3) ... Purging configuration files for r-base-core (4.4.1-1) ... 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 (8.2-4) ... 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 (3.0043+nmu1) ... dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for unzip (6.0-28) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.19) ... dpkg: warning: ignoring request to remove zip which isn't installed 3m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72: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', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', '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-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-yaml', 'python3-zipp', 'python3.12', 'python3.12-minimal', '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'] 3m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--purge', 'cnvkit'] 3m44.1s DUMP: dpkg: warning: ignoring request to remove cnvkit which isn't installed 3m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--purge', 'cnvkit'] 3m44.1s INFO: Running scripts post_purge 3m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_purge_exceptions'] 3m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_purge_exceptions'] 3m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--purge', '--pending'] 3m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--purge', '--pending'] 3m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--remove', '--pending'] 3m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg', '--remove', '--pending'] 3m44.1s INFO: Running scripts post_test 3m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_test_exceptions'] 3m44.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'tmp/scripts/post_test_exceptions'] 3m44.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 3m44.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 3m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg-divert', '--list'] 3m44.5s 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 3m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'dpkg-divert', '--list'] 3m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'clean'] 3m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy', 'apt-get', 'clean'] 3m44.6s DEBUG: Recording chroot state 3m45.2s 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 3m45.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/shm'] 3m45.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/shm'] 3m45.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/console'] 3m45.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/console'] 3m45.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/ptmx'] 3m45.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/ptmx'] 3m45.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/pts'] 3m45.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/dev/pts'] 3m45.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/proc'] 3m45.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy/proc'] 3m45.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 3m45.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzeuej9cy'] 3m45.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpzeuej9cy 3m45.8s INFO: PASS: Upgrading between Debian distributions. 3m45.8s INFO: PASS: All tests. 3m45.8s INFO: piuparts run ends. ret=0 End: 2024-07-22 21:13:25 GMT