Start: 2024-08-23 04:12:52 GMT [bookworm] Package: cnvkit Source: cnvkit (0.9.9-2) Version: 0.9.9-2+b1 Installed-Size: 69065 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-joblib, python3-matplotlib, python3-networkx, 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: http://cnvkit.readthedocs.org Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.9-2+b1_amd64.deb Size: 15425488 MD5sum: 5cfed4dd3f195add8141e1a3bf795500 SHA256: b773bb7977d6fc9462b53b684aa74b7bd980387e48df07461a504d12742fcda0 [bookworm-next] Package: cnvkit Source: cnvkit (0.9.9-2) Version: 0.9.9-2+b1 Installed-Size: 69065 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-joblib, python3-matplotlib, python3-networkx, 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: http://cnvkit.readthedocs.org Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.9-2+b1_amd64.deb Size: 15425488 MD5sum: 5cfed4dd3f195add8141e1a3bf795500 SHA256: b773bb7977d6fc9462b53b684aa74b7bd980387e48df07461a504d12742fcda0 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt cnvkit=0.9.9-2+b1 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 1.4.4~202408201642~1.4.3-11-g36a88c35 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt cnvkit=0.9.9-2+b1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpebcy3vlo 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpebcy3vlo 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpebcy3vlo/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'update'] 0m1.2s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'update'] 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s INFO: Running scripts post_setup 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 0m3.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 0m3.4s INFO: Running scripts is_testable 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s INFO: Running scripts pre_test 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_test_root_password'] 0m3.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_test_root_password'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m3.6s DUMP: Package: cnvkit Source: cnvkit (0.9.9-2) Version: 0.9.9-2+b1 Installed-Size: 69065 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-joblib, python3-matplotlib, python3-networkx, 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: http://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.9-2+b1_amd64.deb Size: 15425488 MD5sum: 5cfed4dd3f195add8141e1a3bf795500 SHA256: b773bb7977d6fc9462b53b684aa74b7bd980387e48df07461a504d12742fcda0 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m3.6s INFO: apt-cache knows about the following packages: cnvkit 0m3.6s INFO: Running scripts pre_install 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy'] 0m3.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy', 'cnvkit'] 0m3.8s DUMP: cnvkit: Installed: (none) Candidate: 0.9.9-2+b1 Version table: 0.9.9-2+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy', 'cnvkit'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-y', 'install', 'cnvkit'] 1m45.5s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 fontconfig fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libexpat1-dev libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 liblsan0 libmpc3 libmpfr6 libncursesw6 libnghttp2-14 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.36 libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libxt6 libyaml-0-2 linux-libc-dev mailcap media-types mime-support openssl perl perl-modules-5.36 procps python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-joblib python3-kiwisolver python3-lib2to3 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-ply python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-yaml python3.11 python3.11-dev python3.11-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common rpcsvc-proto 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 zlib1g-dev Suggested packages: binutils-doc blt-demo cpp-doc gcc-12-locales cpp-12-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib g++-12-multilib gcc-12-doc gcc-multilib make manpages-dev autoconf automake libtool flex bison gdb gcc-doc gcc-12-multilib libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc gdbm-l10n low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils libstdc++-12-doc tcl8.6 tk8.6 libxsimd-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python-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 gfortran python3-pytest python-pandas-doc python3-statsmodels python-pil-doc python3-setuptools python-ply-doc python-pomegranate-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.11-venv python3.11-doc 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: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase psmisc python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-bs4 python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-jinja2 python3-numba python3-olefile python3-nose 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: binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cnvkit cpp cpp-12 fontconfig fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libexpat1-dev libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 liblsan0 libmpc3 libmpfr6 libncursesw6 libnghttp2-14 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.36 libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libxt6 libyaml-0-2 linux-libc-dev mailcap media-types mime-support openssl perl perl-modules-5.36 procps python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-joblib python3-kiwisolver python3-lib2to3 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-ply python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-yaml python3.11 python3.11-dev python3.11-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common rpcsvc-proto 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 zlib1g-dev 0 upgraded, 228 newly installed, 0 to remove and 0 not upgraded. Need to get 265 MB of archives. After this operation, 1219 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:18 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:29 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 binutils-common amd64 2.40-2 [2487 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libbinutils amd64 2.40-2 [572 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libctf-nobfd0 amd64 2.40-2 [153 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libctf0 amd64 2.40-2 [89.8 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libgprofng0 amd64 2.40-2 [812 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libjansson4 amd64 2.14-2 [40.8 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2 [2246 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 binutils amd64 2.40-2 [65.0 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:53 http://deb.debian.org/debian 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Get:64 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+deb12u1 [74.2 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+deb12u1 [472 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 python3-joblib all 1.2.0-4 [211 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get:113 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libisl23 amd64 0.25-1.1 [683 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 cpp amd64 4:12.2.0-3 [6836 B] Get:120 http://deb.debian.org/debian bookworm/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:123 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB] Get:129 http://deb.debian.org/debian bookworm/main amd64 gcc amd64 4:12.2.0-3 [5216 B] Get:130 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u7 [45.8 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.94-1 [1994 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u7 [1899 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB] Get:139 http://deb.debian.org/debian bookworm/main amd64 g++ amd64 4:12.2.0-3 [1356 B] Get:140 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:145 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6+deb12u2 [1987 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6+deb12u2 [4742 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get:150 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get:151 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get:154 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6+deb12u2 [615 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get:159 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get:161 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get:162 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get:166 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 python3-pomegranate amd64 0.14.8-3+b1 [2509 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 python3-pyfaidx all 0.7.1-2 [28.0 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u6 [385 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 python3-sklearn-lib amd64 1.2.1+dfsg-1 [2567 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 python3-sklearn all 1.2.1+dfsg-1 [2103 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:209 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u6 [390 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:226 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 r-bioc-dnacopy amd64 1.72.3-1 [377 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 cnvkit amd64 0.9.9-2+b1 [15.4 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 265 MB in 2s (142 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 6093 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../3-libperl5.36_5.36.0-7+deb12u1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7+deb12u1) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl (5.36.0-7+deb12u1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../5-libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../6-libpython3.11-minimal_3.11.2-6+deb12u2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../7-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../8-python3.11-minimal_3.11.2-6+deb12u2_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6+deb12u2) ... Setting up libssl3:amd64 (3.0.13-1~deb12u1) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6+deb12u2) ... 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 ... 8425 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../02-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... 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Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libjansson4:amd64 (2.14-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up zip (3.0-13) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libmpfr6:amd64 (4.2.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libmpc3:amd64 (1.3.1-1) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libasan8:amd64 (12.2.0-14) ... Setting up procps (2:4.0.2-3) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libtsan2:amd64 (12.2.0-14) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.40-2) ... Setting up libisl23:amd64 (0.25-1.1) ... Setting up libc-dev-bin (2.36-9+deb12u7) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... 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 libcc1-0:amd64 (12.2.0-14) ... Setting up liblsan0:amd64 (12.2.0-14) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libctf0:amd64 (2.40-2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up cpp-12 (12.2.0-14) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libgprofng0:amd64 (2.40-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up cpp (4:12.2.0-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u6) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up binutils-x86-64-linux-gnu (2.40-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u6) ... Setting up binutils (2.40-2) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up gcc-12 (12.2.0-14) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up mailcap (3.70+nmu1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up mime-support (3.66) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up gcc (4:12.2.0-3) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u7) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up libpython3.11:amd64 (3.11.2-6+deb12u2) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up r-bioc-dnacopy (1.72.3-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up g++-12 (12.2.0-14) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-pyfaidx (0.7.1-2) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-joblib (1.2.0-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3-ply (3.11-5) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+deb12u1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6+deb12u2) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up g++ (4:12.2.0-3) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3.11-dev (3.11.2-6+deb12u2) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-sklearn-lib:amd64 (1.2.1+dfsg-1) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-pomegranate (0.14.8-3+b1) ... Setting up python3-sklearn (1.2.1+dfsg-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Setting up cnvkit (0.9.9-2+b1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-y', 'install', 'cnvkit'] 1m45.5s INFO: Running scripts post_install 1m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_install_exceptions'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_install_exceptions'] 1m45.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 1m48.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 1m48.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpebcy3vlo to bookworm-next 1m48.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 1m48.2s INFO: Running scripts pre_distupgrade 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_exceptions'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_exceptions'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'update'] 1m49.8s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [111 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [64.4 kB] Fetched 650 kB in 1s (936 kB/s) Reading package lists... 1m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'update'] 1m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-yf', 'dist-upgrade'] 1m55.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 linux-libc-dev openssl python3-numpy 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 16.8 MB of archives. After this operation, 1592 kB disk space will be freed. Get:1 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6-dev amd64 2.36-9+deb12u8 [1900 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-dev-bin amd64 2.36-9+deb12u8 [46.3 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 linux-libc-dev amd64 6.1.106-2 [2027 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:11 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:12 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.14-1~deb12u1 [2024 kB] Get:13 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.14-1~deb12u1 [1423 kB] Get:14 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.8 MB in 0s (132 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 ... 45750 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.36-9+deb12u8_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../libc-dev-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../linux-libc-dev_6.1.106-2_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.106-2) over (6.1.94-1) ... Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (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 ... 45750 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (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 ... 45750 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (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 ... 45750 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (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 ... 45750 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.14-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.14-1~deb12u1) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssl_3.0.14-1~deb12u1_amd64.deb ... Unpacking openssl (3.0.14-1~deb12u1) over (3.0.13-1~deb12u1) ... Preparing to unpack .../6-python3-numpy_1%3a1.24.2-1+deb12u1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1+deb12u1) over (1:1.24.2-1) ... Setting up libssl3:amd64 (3.0.14-1~deb12u1) ... Setting up linux-libc-dev:amd64 (6.1.106-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up python3-numpy (1:1.24.2-1+deb12u1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up libc-dev-bin (2.36-9+deb12u8) ... Setting up openssl (3.0.14-1~deb12u1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u8) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 1m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-yf', 'dist-upgrade'] 1m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m56.0s DUMP: a7383adc5fdea12f93db4552c396e73a - 1m56.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m56.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 1m56.2s DUMP: Package: cnvkit Source: cnvkit (0.9.9-2) Version: 0.9.9-2+b1 Installed-Size: 69065 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-joblib, python3-matplotlib, python3-networkx, 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: http://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.9-2+b1_amd64.deb Size: 15425488 MD5sum: 5cfed4dd3f195add8141e1a3bf795500 SHA256: b773bb7977d6fc9462b53b684aa74b7bd980387e48df07461a504d12742fcda0 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 1m56.2s INFO: apt-cache knows about the following packages: cnvkit 1m56.2s INFO: Running scripts pre_install 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_database-server'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_database-server'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_exceptions'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_exceptions'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_extras'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_extras'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy'] 1m56.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy'] 1m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy', 'cnvkit'] 1m56.3s DUMP: cnvkit: Installed: 0.9.9-2+b1 Candidate: 0.9.9-2+b1 Version table: *** 0.9.9-2+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy', 'cnvkit'] 1m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-y', 'install', 'cnvkit'] 1m56.7s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.9-2+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-y', 'install', 'cnvkit'] 1m56.7s INFO: Running scripts post_install 1m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_install_exceptions'] 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_install_exceptions'] 1m56.7s INFO: Running scripts post_distupgrade 1m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_exceptions'] 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_exceptions'] 1m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_zz_backports'] 1m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_distupgrade_zz_backports'] 1m56.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 1m59.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 1m59.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 2m1.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 2m1.8s INFO: Running scripts pre_install 2m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_database-server'] 2m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_database-server'] 2m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_exceptions'] 2m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_exceptions'] 2m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_extras'] 2m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_extras'] 2m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture'] 2m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture'] 2m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy'] 2m1.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy'] 2m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy', 'cnvkit'] 2m1.9s DUMP: cnvkit: Installed: 0.9.9-2+b1 Candidate: 0.9.9-2+b1 Version table: *** 0.9.9-2+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 2m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-cache', 'policy', 'cnvkit'] 2m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-y', 'install', 'cnvkit=0.9.9-2+b1'] 2m2.2s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.9-2+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', '-y', 'install', 'cnvkit=0.9.9-2+b1'] 2m2.2s INFO: Running scripts post_install 2m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_install_exceptions'] 2m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_install_exceptions'] 2m2.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 2m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 2m4.8s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 2m4.9s INFO: /bin converted to /usr/bin by /usr merge 2m4.9s INFO: /lib converted to /usr/lib by /usr merge 2m4.9s INFO: /lib/init converted to /usr/lib/init by /usr merge 2m4.9s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 2m4.9s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 2m4.9s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 2m4.9s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 2m4.9s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 2m4.9s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 2m4.9s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 2m4.9s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 2m4.9s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 2m4.9s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 2m4.9s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 2m4.9s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 2m4.9s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 2m4.9s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 2m4.9s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 2m4.9s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 2m4.9s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 2m4.9s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 2m4.9s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 2m4.9s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 2m4.9s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 2m4.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m4.9s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 2m4.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m4.9s INFO: /sbin converted to /usr/sbin by /usr merge 2m7.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', '-ac', '--ignore-obsolete'] 2m12.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', '-ac', '--ignore-obsolete'] 2m12.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m12.1s DUMP: 0.15.6 2m12.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m12.1s INFO: Running adequate version 0.15.6 now. 2m12.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'cnvkit'] 2m12.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'cnvkit'] 2m12.3s INFO: Running scripts pre_remove 2m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_exceptions'] 2m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/pre_remove_exceptions'] 2m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m19.2s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed binutils binutils 2.40-2 install ok installed binutils-common:amd64 binutils-common 2.40-2 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.40-2 install ok installed blt blt 2.5.3+dfsg-4.1 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed ca-certificates ca-certificates 20230311 install ok installed cnvkit cnvkit 0.9.9-2+b1 install ok installed coreutils coreutils 9.1-1 install ok installed cpp cpp 4:12.2.0-3 install ok installed cpp-12 cpp-12 12.2.0-14 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig fontconfig 2.14.1-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 install ok installed fonts-lyx fonts-lyx 2.3.7-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed g++ g++ 4:12.2.0-3 install ok installed g++-12 g++-12 12.2.0-14 install ok installed gcc gcc 4:12.2.0-3 install ok installed gcc-12 gcc-12 12.2.0-14 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libasan8:amd64 libasan8 12.2.0-14 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libbinutils:amd64 libbinutils 2.40-2 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0+ds1-21 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc-dev-bin libc-dev-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libc6-dev:amd64 libc6-dev 2.36-9+deb12u8 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcc1-0:amd64 libcc1-0 12.2.0-14 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.33-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.40-2 install ok installed libctf0:amd64 libctf0 2.40-2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.88.1-10+deb12u6 install ok installed libcurl4:amd64 libcurl4 7.88.1-10+deb12u6 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-2+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.2.0-14 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgprofng0:amd64 libgprofng0 2.40-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.16+ds-3 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.3.0-4 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libisl23:amd64 libisl23 0.25-1.1 install ok installed libitm1:amd64 libitm1 12.2.0-14 install ok installed libjansson4:amd64 libjansson4 2.14-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 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 libjs-sphinxdoc libjs-sphinxdoc 5.3.0-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblsan0:amd64 liblsan0 12.2.0-14 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libmpc3:amd64 libmpc3 1.3.1-1 install ok installed libmpfr6:amd64 libmpfr6 4.2.0-1 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.52.0-1+deb12u1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.21+ds-4 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.21+ds-4 install ok installed libopenblas0:amd64 libopenblas0 0.3.21+ds-4 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.21+ds-4 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.50.12+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.50.12+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.50.12+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.2-3 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.11.2-1+b1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.2-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11:amd64 libpython3.11 3.11.2-6+deb12u2 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.2-6+deb12u2 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-5 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libraqm0:amd64 libraqm0 0.7.0-4.1 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.14-1~deb12u1 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.2.0-14 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-1 install ok installed libthai0:amd64 libthai0 0.1.29-1 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtsan2:amd64 libtsan2 12.2.0-14 install ok installed libubsan1:amd64 libubsan1 12.2.0-14 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.4-0.2+deb12u1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.4-0.2+deb12u1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3~deb12u1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxsimd-dev:amd64 libxsimd-dev 8.1.0-7 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed linux-libc-dev:amd64 linux-libc-dev 6.1.106-2 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed openssl openssl 3.0.14-1~deb12u1 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed procps procps 2:4.0.2-3 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-all python3-all 3.11.2-1+b1 install ok installed python3-all-dev python3-all-dev 3.11.2-1+b1 install ok installed python3-appdirs python3-appdirs 1.4.4-3 install ok installed python3-attr python3-attr 22.2.0-1 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-biopython python3-biopython 1.80+dfsg-4+b1 install ok installed python3-brotli python3-brotli 1.0.9-2+b6 install ok installed python3-contourpy python3-contourpy 1.0.7-1+b1 install ok installed python3-cycler python3-cycler 0.11.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-2 install ok installed python3-decorator python3-decorator 5.1.1-3 install ok installed python3-dev python3-dev 3.11.2-1+b1 install ok installed python3-distutils python3-distutils 3.11.2-3 install ok installed python3-fonttools python3-fonttools 4.38.0-1+b1 install ok installed python3-fs python3-fs 2.4.16-2 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-joblib python3-joblib 1.2.0-4 install ok installed python3-kiwisolver python3-kiwisolver 1.4.4-1+b1 install ok installed python3-lib2to3 python3-lib2to3 3.11.2-3 install ok installed python3-lxml:amd64 python3-lxml 4.9.2-1+b1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b2 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1+b1 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-mpmath python3-mpmath 1.2.1-2 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 install ok installed python3-packaging python3-packaging 23.0-1 install ok installed python3-pandas python3-pandas 1.5.3+dfsg-2 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 1.5.3+dfsg-2 install ok installed python3-pil:amd64 python3-pil 9.4.0-1.1+deb12u1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 9.4.0-1.1+deb12u1 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-ply python3-ply 3.11-5 install ok installed python3-pomegranate python3-pomegranate 0.14.8-3+b1 install ok installed python3-pyfaidx python3-pyfaidx 0.7.1-2 install ok installed python3-pyparsing python3-pyparsing 3.0.9-1 install ok installed python3-pysam python3-pysam 0.20.0+ds-3+b1 install ok installed python3-pythran python3-pythran 0.11.0+ds-7 install ok installed python3-renderpm:amd64 python3-renderpm 3.6.12-1+b1 install ok installed python3-reportlab python3-reportlab 3.6.12-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.6.12-1+b1 install ok installed python3-scipy python3-scipy 1.10.1-2 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-sklearn python3-sklearn 1.2.1+dfsg-1 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 1.2.1+dfsg-1 install ok installed python3-sympy python3-sympy 1.11.1-1 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.11.2-3 install ok installed python3-tz python3-tz 2022.7.1-4 install ok installed python3-ufolib2 python3-ufolib2 0.14.0+dfsg1-1 install ok installed python3-yaml python3-yaml 6.0-3+b2 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-dev python3.11-dev 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed r-base-core r-base-core 4.2.2.20221110-2 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.44.0-2 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.72.3-1 install ok installed readline-common readline-common 8.2-1.3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-1 install ok installed sensible-utils sensible-utils 0.0.17+nmu1 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-4.1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.0.0-1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 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 0.18+nmu1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.13.dfsg-1 2m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-12', 'gcc', 'gcc-12', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'procps', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-joblib', 'python3-kiwisolver', 'python3-lib2to3', '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-ply', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-yaml', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'rpcsvc-proto', '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', 'zlib1g-dev:amd64', 'cnvkit'] 3m4.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cnvkit cpp cpp-12 fontconfig fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libexpat1-dev libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 liblsan0 libmpc3 libmpfr6 libncursesw6 libnghttp2-14 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.36 libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libxt6 libyaml-0-2 linux-libc-dev mailcap media-types mime-support openssl perl perl-modules-5.36 procps python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-joblib python3-kiwisolver python3-lib2to3 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-ply python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-yaml python3.11 python3.11-dev python3.11-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common rpcsvc-proto 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 zlib1g-dev 0 upgraded, 0 newly installed, 228 to remove and 0 not upgraded. After this operation, 1218 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 ... 45749 files and directories currently installed.) Removing cnvkit (0.9.9-2+b1) ... Removing python3-sklearn (1.2.1+dfsg-1) ... Removing python3-pomegranate (0.14.8-3+b1) ... Removing g++ (4:12.2.0-3) ... Removing gcc (4:12.2.0-3) ... Removing python3-biopython (1.80+dfsg-4+b1) ... Removing python3-reportlab (3.6.12-1) ... Removing python3-matplotlib (3.6.3-1+b1) ... Removing python3-pil.imagetk:amd64 (9.4.0-1.1+deb12u1) ... Removing python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Removing python3-tk:amd64 (3.11.2-3) ... Removing blt (2.5.3+dfsg-4.1) ... Removing r-bioc-dnacopy (1.72.3-1) ... Removing r-bioc-biocgenerics (0.44.0-2) ... Removing r-base-core (4.2.2.20221110-2) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp (4:12.2.0-3) ... Removing libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpango-1.0-0:amd64 (1.50.12+ds-1) ... Removing fontconfig (2.14.1-4) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libcairo2:amd64 (1.16.0-7) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing python-matplotlib-data (3.6.3-1) ... Removing fonts-dejavu-core (2.37-6) ... Removing fonts-lyx (2.3.7-1) ... Removing python3-renderpm:amd64 (3.6.12-1+b1) ... Removing fonts-urw-base35 (20200910-7) ... Removing python3-sklearn-lib:amd64 (1.2.1+dfsg-1) ... Removing python3-pandas (1.5.3+dfsg-2) ... Removing python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Removing python3-contourpy (1.0.7-1+b1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libcurl4:amd64 (7.88.1-10+deb12u6) ... Removing python3-pysam (0.20.0+ds-3+b1) ... Removing libhts3:amd64 (1.16+ds-3) ... Removing libcurl3-gnutls:amd64 (7.88.1-10+deb12u6) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.29-1) ... Removing libdatrie1:amd64 (0.2.13-2+b1) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing python3-yaml (6.0-3+b2) ... Removing xfonts-utils (1:7.7+6) ... Removing libfontenc1:amd64 (1:1.1.4-1) ... Removing libraqm0:amd64 (0.7.0-4.1) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.36.0-7+deb12u1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libopenblas-dev:amd64 (0.3.21+ds-4) ... Removing libopenblas0:amd64 (0.3.21+ds-4) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libhtscodecs2:amd64 (1.3.0-4) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing python3-joblib (1.2.0-4) ... Removing procps (2:4.0.2-3) ... Removing libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Removing libopenjp2-7:amd64 (2.5.0-2) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libproc2-0:amd64 (2:4.0.2-3) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing libqhull-r8.0:amd64 (2020.2-5) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-10) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing openssl (3.0.14-1~deb12u1) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libthai-data (0.1.29-1) ... Removing libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libyaml-0-2:amd64 (0.2.5-1) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing python3-cycler (0.11.0-1) ... Removing python3-dateutil (2.8.2-2) ... Removing python3-kiwisolver (1.4.4-1+b1) ... Removing python3-networkx (2.8.8-1) ... Removing python3-packaging (23.0-1) ... Removing python3-pyfaidx (0.7.1-2) ... Removing python3-pyparsing (3.0.9-1) ... Removing python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.17+nmu1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... 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) ... 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 libbrotli1:amd64 (1.0.9-2+b6) ... Removing libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing python3-fonttools (4.38.0-1+b1) ... Removing python3-sympy (1.11.1-1) ... Removing python3-lxml:amd64 (4.9.2-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Removing libicu72:amd64 (72.1-3) ... Removing python3-fs (2.4.16-2) ... Removing python3-appdirs (1.4.4-3) ... Removing python3-brotli (1.0.9-2+b6) ... Removing python3-lz4 (4.0.2+dfsg-1+b2) ... Removing python3-mpmath (1.2.1-2) ... Removing python3-six (1.16.0-4) ... Removing python3-tz (2022.7.1-4) ... Removing unicode-data (15.0.0-1) ... Removing python3-scipy (1.10.1-2) ... Removing python3-pythran (0.11.0+ds-7) ... Removing g++-12 (12.2.0-14) ... Removing libboost-dev:amd64 (1.74.0.3) ... Removing libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Removing libstdc++-12-dev:amd64 (12.2.0-14) ... Removing python3-numpy (1:1.24.2-1+deb12u1) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Removing python3-all-dev (3.11.2-1+b1) ... Removing python3-dev (3.11.2-1+b1) ... Removing python3.11-dev (3.11.2-6+deb12u2) ... Removing libpython3-all-dev:amd64 (3.11.2-1+b1) ... Removing libpython3-dev:amd64 (3.11.2-1+b1) ... Removing libpython3.11-dev:amd64 (3.11.2-6+deb12u2) ... Removing zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Removing libexpat1-dev:amd64 (2.5.0-1) ... Removing libc6-dev:amd64 (2.36-9+deb12u8) ... Removing libc-dev-bin (2.36-9+deb12u8) ... Removing libcrypt-dev:amd64 (1:4.4.33-2) ... Removing python3-ufolib2 (0.14.0+dfsg1-1) ... Removing python3-all (3.11.2-1+b1) ... Removing python3-distutils (3.11.2-3) ... Removing libpython3.11:amd64 (3.11.2-6+deb12u2) ... Removing libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... Removing libopenblas0-pthread:amd64 (0.3.21+ds-4) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libnsl-dev:amd64 (1.3.0-2) ... Removing libtirpc-dev:amd64 (1.3.3+ds-1) ... Removing libjs-sphinxdoc (5.3.0-4) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing libxsimd-dev:amd64 (8.1.0-7) ... Removing linux-libc-dev:amd64 (6.1.106-2) ... Removing python3-attr (22.2.0-1) ... Removing python3-beniget (0.4.1-3) ... Removing python3-decorator (5.1.1-3) ... Removing python3-gast (0.5.2-2) ... Removing python3-lib2to3 (3.11.2-3) ... Removing python3-pkg-resources (66.1.1-1) ... Removing python3-ply (3.11-5) ... Removing rpcsvc-proto (1.4.3-1) ... Removing gcc-12 (12.2.0-14) ... Removing binutils (2.40-2) ... Removing binutils-x86-64-linux-gnu (2.40-2) ... Removing libgprofng0:amd64 (2.40-2) ... Removing libctf0:amd64 (2.40-2) ... Removing libbinutils:amd64 (2.40-2) ... Removing binutils-common:amd64 (2.40-2) ... Removing cpp-12 (12.2.0-14) ... Removing libgcc-12-dev:amd64 (12.2.0-14) ... Removing libasan8:amd64 (12.2.0-14) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing libcc1-0:amd64 (12.2.0-14) ... Removing libctf-nobfd0:amd64 (2.40-2) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libgomp1:amd64 (12.2.0-14) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libisl23:amd64 (0.25-1.1) ... Removing libitm1:amd64 (12.2.0-14) ... Removing libjansson4:amd64 (2.14-2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing liblsan0:amd64 (12.2.0-14) ... Removing libmpc3:amd64 (1.3.1-1) ... Removing libmpfr6:amd64 (4.2.0-1) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libssl3:amd64 (3.0.14-1~deb12u1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libtsan2:amd64 (12.2.0-14) ... Removing libubsan1:amd64 (12.2.0-14) ... Removing media-types (10.0.0) ... Removing readline-common (8.2-1.3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 3m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-12', 'gcc', 'gcc-12', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'procps', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-joblib', 'python3-kiwisolver', 'python3-lib2to3', '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-ply', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-yaml', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'rpcsvc-proto', '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', 'zlib1g-dev:amd64', 'cnvkit'] 3m4.3s INFO: Running scripts post_remove 3m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_remove_exceptions'] 3m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_remove_exceptions'] 3m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'gcc', 'gcc-12', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'procps', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-joblib', 'python3-kiwisolver', 'python3-lib2to3', '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-ply', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-yaml', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'rpcsvc-proto', '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', 'zlib1g-dev:amd64'] 3m5.4s DUMP: dpkg: warning: ignoring request to remove binutils which isn't installed (Reading database ... 6167 files and directories currently installed.) Purging configuration files for binutils-common:amd64 (2.40-2) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove blt which isn't installed Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cpp which isn't installed dpkg: warning: ignoring request to remove cpp-12 which isn't installed Purging configuration files for fontconfig (2.14.1-4) ... Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-7) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-12 which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-12 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.74-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.33-2) ... dpkg: warning: ignoring request to remove libctf-nobfd0 which isn't installed dpkg: warning: ignoring request to remove libctf0 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 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 libexpat1-dev 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 libgcc-12-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgprofng0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 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 libisl23 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjansson4 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 libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore 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 liblsan0 which isn't installed dpkg: warning: ignoring request to remove libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 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 libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenblas-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-pthread-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread 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) ... dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-all-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.11 which isn't installed dpkg: warning: ignoring request to remove libpython3.11-dev which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed 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 libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev 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 (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 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 libxsimd-dev 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 libxt6 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for openssl (3.0.14-1~deb12u1) ... Purging configuration files for perl (5.36.0-7+deb12u1) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for procps (2:4.0.2-3) ... Purging configuration files for python-matplotlib-data (3.6.3-1) ... Purging configuration files for python3 (3.11.2-1+b1) ... dpkg: warning: ignoring request to remove python3-all which isn't installed dpkg: warning: ignoring request to remove python3-all-dev which isn't installed 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-beniget 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-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-dev which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-gast 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-lib2to3 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-ply 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-pythran which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel 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 (1.11.1-1) ... 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-yaml which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed dpkg: warning: ignoring request to remove python3.11-dev which isn't installed Purging configuration files for python3.11-minimal (3.11.2-6+deb12u2) ... Purging configuration files for r-base-core (4.2.2.20221110-2) ... 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 (8.2-1.3) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed 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) ... 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 (0.18+nmu1) ... dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 3m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'gcc', 'gcc-12', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'procps', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-joblib', 'python3-kiwisolver', 'python3-lib2to3', '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-ply', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-yaml', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'rpcsvc-proto', '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', 'zlib1g-dev:amd64'] 3m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--purge', 'cnvkit'] 3m5.5s DUMP: dpkg: warning: ignoring request to remove cnvkit which isn't installed 3m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--purge', 'cnvkit'] 3m5.5s INFO: Running scripts post_purge 3m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_purge_exceptions'] 3m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_purge_exceptions'] 3m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--purge', '--pending'] 3m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--purge', '--pending'] 3m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--remove', '--pending'] 3m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg', '--remove', '--pending'] 3m5.5s INFO: Running scripts post_test 3m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_test_exceptions'] 3m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'tmp/scripts/post_test_exceptions'] 3m5.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 3m6.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 3m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg-divert', '--list'] 3m6.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 3m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'dpkg-divert', '--list'] 3m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'clean'] 3m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo', 'apt-get', 'clean'] 3m6.1s DEBUG: Recording chroot state 3m7.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/shm'] 3m7.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/shm'] 3m7.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/console'] 3m7.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/console'] 3m7.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/ptmx'] 3m7.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/ptmx'] 3m7.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/pts'] 3m7.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/dev/pts'] 3m7.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/proc'] 3m7.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo/proc'] 3m7.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 3m7.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpebcy3vlo'] 3m7.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpebcy3vlo 3m7.3s INFO: PASS: Upgrading between Debian distributions. 3m7.3s INFO: PASS: All tests. 3m7.3s INFO: piuparts run ends. ret=0 End: 2024-08-23 04:15:59 GMT