Start: 2024-04-08 15:52:11 GMT [testing] 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 [sid] Package: cnvkit Version: 0.9.10-2 Installed-Size: 94731 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description: Copy number variant detection from targeted DNA sequencing Homepage: https://cnvkit.readthedocs.org Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.10-2_all.deb Size: 19501620 MD5sum: 34bc5101407f83474714510d690c42f5 SHA256: bf1fd75c757a204fb8123b69285b16b389dfc0c840d3941227ff8c7f89a602e3 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt cnvkit=0.9.10-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt cnvkit=0.9.10-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpl1e1234q 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpl1e1234q 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpl1e1234q/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s 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 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s 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' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s 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+deb12u5 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 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+b1 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+deb12u4 install ok installed libc6:amd64 libc6 2.36-9+deb12u4 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+deb12u2 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+b1 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+b3 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+b1 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 252.22-1~deb12u1 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 252.22-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 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+b1 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+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 0m3.9s INFO: Running scripts is_testable 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s INFO: Running scripts pre_test 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_test_root_password'] 0m3.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_test_root_password'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m4.1s 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 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m4.1s INFO: apt-cache knows about the following packages: cnvkit 0m4.1s INFO: Running scripts pre_install 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_database-server'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_database-server'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy'] 0m4.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy', 'cnvkit'] 0m4.3s 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 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy', 'cnvkit'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', 'install', 'cnvkit'] 2m18.5s 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 3.0.11-1~deb12u2 [2019 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 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 [2064 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 [1796 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 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 3.0.11-1~deb12u2 [1419 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 [399 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 bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:55 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] 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+b1 [74.4 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 [1398 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+b1 [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+deb12u4 [45.4 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.76-1 [1930 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+deb12u4 [1897 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 [1988 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 [4738 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 [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+deb12u5 [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+deb12u5 [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 9s (29.5 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 ... 6102 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_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../6-libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... 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_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 8434 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 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+deb12u4) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.11-1~deb12u2) ... 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) ... 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+deb12u5) ... 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+deb12u5) ... 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) ... 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+deb12u4) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... 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) ... 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+b1) ... 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+b1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... 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) ... 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+deb12u4) ... 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. 2m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', 'install', 'cnvkit'] 2m18.5s INFO: Running scripts post_install 2m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_install_exceptions'] 2m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_install_exceptions'] 2m18.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 2m20.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 2m20.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpl1e1234q to sid 2m20.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 2m20.1s INFO: Running scripts pre_distupgrade 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_exceptions'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_exceptions'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', 'update'] 2m25.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9909 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7192 kB] Fetched 17.3 MB in 4s (4743 kB/s) Reading package lists... 2m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', 'update'] 2m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-yf', 'dist-upgrade'] 5m11.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libboost-dev libboost1.83-dev libglib2.0-0 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36 libpython3-all-dev libpython3.12-dev libpython3.12t64 libtirpc-dev libxsimd-dev perl-modules-5.36 python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev xtl-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libboost1.74-dev libcurl3-gnutls libcurl4 libdb5.3 libext2fs2 libgdbm-compat4 libgdbm6 libgnutls30 libhogweed6 libhts3 libnettle8 libpng16-16 libpsl5 libpython3.11 libreadline8 libssh2-1 libssl3 libtirpc3 libxt6 python3-renderpm python3-reportlab-accel The following NEW packages will be installed: cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu fonts-dejavu-mono g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libboost1.83-dev libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libext2fs2t64 libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libhogweed6t64 libhts3t64 libhwasan0 libnettle8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libpython3.11t64 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libreadline8t64 libsframe1 libsharpyuv0 libssh2-1t64 libssl3t64 libstdc++-13-dev libtirpc3t64 libunistring5 libxt6t64 netbase perl-modules-5.38 python3-cairo python3-chardet python3-freetype python3-importlib-metadata python3-more-itertools python3-rlpycairo python3-setuptools python3-zipp python3.12 python3.12-dev python3.12-minimal xtl-dev The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu blt bsdutils ca-certificates cnvkit coreutils cpp cpp-12 dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblas3 libblkid1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdatrie1 libdebconfclient0 libdeflate0 libexpat1 libexpat1-dev libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-s1 libgcrypt20 libgfortran5 libglib2.0-0 libgmp10 libgomp1 libgpg-error0 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhtscodecs2 libicu72 libidn2-0 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-sphinxdoc libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnghttp2-14 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre2-8-0 libpixman-1-0 libproc2-0 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libstdc++-12-dev libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan2 libubsan1 libudev1 libuuid1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxft2 libxml2 libxsimd-dev libxxhash0 libzstd1 linux-libc-dev login logsave mawk media-types mount ncurses-base ncurses-bin openssl passwd perl perl-base procps python3 python3-all python3-all-dev python3-appdirs python3-attr python3-biopython python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs 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-reportlab python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-sympy 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 sed sensible-utils sysvinit-utils tar tk8.6-blt2.5 tzdata unicode-data usr-is-merged util-linux util-linux-extra xml-core zlib1g zlib1g-dev 258 upgraded, 58 newly installed, 22 to remove and 0 not upgraded. Need to get 384 MB of archives. After this operation, 538 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-11 [97.4 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3+b2 [67.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15.1 [1905 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15.1 [47.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.2 [10.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.2 [189 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.7.1-2 [440 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:17 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get:18 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:19 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:20 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:21 http://deb.debian.org/debian sid/main amd64 python3.11-dev amd64 3.11.8-3+b3 [501 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpython3.11-dev amd64 3.11.8-3+b3 [4513 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libpython3.11t64 amd64 3.11.8-3+b3 [1958 kB] Get:26 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:27 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-3+b3 [597 kB] Get:28 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3+b3 [1879 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3+b3 [1792 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3+b3 [817 kB] Get:31 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:33 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:36 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [697 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1+b1 [73.0 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1+b1 [48.8 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2+b2 [4279 kB] Get:41 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2+b2 [236 kB] Get:42 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2+b2 [1644 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:45 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:46 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-2 [255 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:48 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [240 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.2-1 [895 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:53 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-2 [61.4 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b2 [74.9 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:66 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240330-1 [43.2 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240330-1 [71.9 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240330-1 [713 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.5-1 [1437 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.14 [986 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b3 [10.2 kB] Get:78 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:80 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b3 [90.3 kB] Get:82 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:83 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:84 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-3 [649 kB] Get:85 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:87 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.14 [1370 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:96 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.61.0-1 [75.3 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.7.1-2 [432 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-6 [275 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-11 [160 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-11 [191 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-6 [1222 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b3 [439 kB] Get:107 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:108 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:109 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:110 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3 [530 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.26+ds-1 [4780 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.26+ds-1 [6807 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.26+ds-1 [37.5 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.26+ds-1 [50.5 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240330-1 [136 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:127 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get:133 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:142 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:146 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:147 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-3+b1 [26.8 MB] Get:148 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.2 [82.6 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:150 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.7.9-2 [2255 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:153 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:154 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:155 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:156 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:157 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:158 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:159 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:160 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:161 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:162 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:163 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:164 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-11 [117 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-11 [30.2 kB] Get:167 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-11 [155 kB] Get:168 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-11 [1231 kB] Get:169 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 39 [5572 B] Get:170 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:171 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:172 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:173 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-23 [44.6 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14-20240330-1 [25.8 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240330-1 [9216 B] Get:176 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14-20240330-1 [2724 kB] Get:177 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14-20240330-1 [1201 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libisl23 amd64 0.26-3+b2 [652 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libmpc3 amd64 1.3.1-1+b2 [52.1 kB] Get:181 http://deb.debian.org/debian sid/main amd64 g++-12 amd64 12.3.0-17 [10.8 MB] Get:182 http://deb.debian.org/debian sid/main amd64 gcc-12 amd64 12.3.0-17 [19.6 MB] Get:183 http://deb.debian.org/debian sid/main amd64 cpp-12 amd64 12.3.0-17 [9859 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14-20240330-1 [1071 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.3.0-17 [2077 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240330-1 [147 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libcc1-0 amd64 14-20240330-1 [42.1 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.3.0-17 [2433 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14-20240330-1 [2454 kB] Get:190 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-17 [42.6 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libgprofng0 amd64 2.42-4 [772 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libctf0 amd64 2.42-4 [87.0 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libctf-nobfd0 amd64 2.42-4 [152 kB] Get:194 http://deb.debian.org/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4 [2215 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libbinutils amd64 2.42-4 [520 kB] Get:196 http://deb.debian.org/debian sid/main amd64 binutils amd64 2.42-4 [80.9 kB] Get:197 http://deb.debian.org/debian sid/main amd64 binutils-common amd64 2.42-4 [2539 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libjansson4 amd64 2.14-2+b2 [39.9 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libsframe1 amd64 2.42-4 [76.0 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14-20240330-1 [1485 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-23 [2537 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-23 [2264 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:204 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get:205 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.4 [20.1 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.4 [206 kB] Get:207 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.4 [571 kB] Get:208 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.83+dfsg1-1 [1634 kB] Get:209 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.1.0-4 [1113 kB] Get:210 http://deb.debian.org/debian sid/main amd64 python3-all-dev amd64 3.11.8-1 [1072 B] Get:211 http://deb.debian.org/debian sid/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get:212 http://deb.debian.org/debian sid/main amd64 cnvkit all 0.9.10-2 [19.5 MB] Get:213 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.1.4+dfsg-7 [3015 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libpython3-all-dev amd64 3.11.8-1 [1072 B] Get:215 http://deb.debian.org/debian sid/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get:216 http://deb.debian.org/debian sid/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get:217 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:218 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:219 http://deb.debian.org/debian sid/main amd64 python3-distutils all 3.12.2-3 [131 kB] Get:220 http://deb.debian.org/debian sid/main amd64 python3-lib2to3 all 3.12.2-3 [77.6 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.2-5 [809 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.2-5 [1951 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libpython3.12t64 amd64 3.12.2-5 [2106 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libpython3.12-dev amd64 3.12.2-5 [5071 kB] Get:226 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.2-5 [2138 kB] Get:227 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.2-5 [653 kB] Get:228 http://deb.debian.org/debian sid/main amd64 python3.12-dev amd64 3.12.2-5 [499 kB] Get:229 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:230 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-6 [5472 kB] Get:231 http://deb.debian.org/debian sid/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get:232 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:234 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.4+b1 [107 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.4+b1 [120 kB] Get:239 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get:240 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get:241 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:242 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:243 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.12.2-3 [108 kB] Get:244 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.1-1 [145 kB] Get:245 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get:246 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:247 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get:248 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:249 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:250 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get:251 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get:252 http://deb.debian.org/debian sid/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get:253 http://deb.debian.org/debian sid/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get:254 http://deb.debian.org/debian sid/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:255 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:256 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:257 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.12-7 [3869 kB] Get:258 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:259 http://deb.debian.org/debian sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:260 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-3 [95.3 kB] Get:261 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:262 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get:263 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get:264 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:265 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get:266 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Get:277 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get:278 http://deb.debian.org/debian sid/main amd64 python3-sklearn-lib amd64 1.4.1.post1+dfsg-1 [6611 kB] Get:279 http://deb.debian.org/debian sid/main amd64 python3-sklearn all 1.4.1.post1+dfsg-1 [2246 kB] Get:280 http://deb.debian.org/debian sid/main amd64 r-bioc-dnacopy amd64 1.76.0-1 [380 kB] Get:281 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:282 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-7 [7883 kB] Get:283 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:284 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:285 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.25.1-2 [140 kB] Get:286 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:287 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:288 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-11 [143 kB] Get:289 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:290 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:291 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:292 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:293 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:294 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:295 http://deb.debian.org/debian sid/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23 [10.3 MB] Get:296 http://deb.debian.org/debian sid/main amd64 g++ amd64 4:13.2.0-7 [1348 B] Get:297 http://deb.debian.org/debian sid/main amd64 gcc amd64 4:13.2.0-7 [5152 B] Get:298 http://deb.debian.org/debian sid/main amd64 cpp amd64 4:13.2.0-7 [1564 B] Get:299 http://deb.debian.org/debian sid/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7 [4724 B] Get:300 http://deb.debian.org/debian sid/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23 [19.8 MB] Get:301 http://deb.debian.org/debian sid/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23 [11.3 MB] Get:302 http://deb.debian.org/debian sid/main amd64 gcc-13 amd64 13.2.0-23 [481 kB] Get:303 http://deb.debian.org/debian sid/main amd64 g++-13 amd64 13.2.0-23 [14.7 kB] Get:304 http://deb.debian.org/debian sid/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7 [1440 B] Get:305 http://deb.debian.org/debian sid/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7 [1200 B] Get:306 http://deb.debian.org/debian sid/main amd64 cpp-13 amd64 13.2.0-23 [1276 B] Get:307 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get:308 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:309 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:310 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2.4 [25.0 kB] Get:311 http://deb.debian.org/debian sid/main amd64 xtl-dev all 0.7.5-3 [89.8 kB] Get:312 http://deb.debian.org/debian sid/main amd64 libxsimd-dev amd64 12.1.1-3 [124 kB] Get:313 http://deb.debian.org/debian sid/main amd64 python3-ply all 3.11-6 [63.7 kB] Get:314 http://deb.debian.org/debian sid/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get:315 http://deb.debian.org/debian sid/main amd64 python3-pythran amd64 0.15.0+ds-2 [443 kB] Get:316 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 384 MB in 3s (115 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45760 files and directories currently installed.) Preparing to unpack .../openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) over (3.0.11-1~deb12u2) ... Preparing to unpack .../zlib1g-dev_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) over (1:1.2.13.dfsg-1) ... Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1) over (1:1.2.13.dfsg-1) ... Setting up zlib1g:amd64 (1:1.3.dfsg-3.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45780 files and directories currently installed.) Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) over (2.4+20151223.gitfa8646d.1-2+b2) ... Preparing to unpack .../python3.11-dev_3.11.8-3+b3_amd64.deb ... Unpacking python3.11-dev (3.11.8-3+b3) over (3.11.2-6) ... Preparing to unpack .../libpython3.11-dev_3.11.8-3+b3_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.8-3+b3) over (3.11.2-6) ... (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 ... 45779 files and directories currently installed.) Removing libpython3.11:amd64 (3.11.2-6) ... (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 ... 45774 files and directories currently installed.) Preparing to unpack .../0-libexpat1-dev_2.6.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.2-1) over (2.5.0-1) ... Preparing to unpack .../1-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) over (2.5.0-1) ... Selecting previously unselected package libpython3.11t64:amd64. Preparing to unpack .../2-libpython3.11t64_3.11.8-3+b3_amd64.deb ... Unpacking libpython3.11t64:amd64 (3.11.8-3+b3) ... Preparing to unpack .../3-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) over (10.0.0) ... Preparing to unpack .../4-python3.11_3.11.8-3+b3_amd64.deb ... Unpacking python3.11 (3.11.8-3+b3) over (3.11.2-6) ... Preparing to unpack .../5-python3.11-minimal_3.11.8-3+b3_amd64.deb ... Unpacking python3.11-minimal (3.11.8-3+b3) over (3.11.2-6) ... Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-3+b3_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.8-3+b3) over (3.11.2-6) ... Preparing to unpack .../7-libpython3.11-minimal_3.11.8-3+b3_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.8-3+b3) over (3.11.2-6) ... Selecting previously unselected package netbase. Preparing to unpack .../8-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libreadline8 (>= 6.0). (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 ... 45807 files and directories currently installed.) Removing libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libreadline8t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45794 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) over (8.2-1.3) ... Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.4-4) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4-4) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45815 files and directories currently installed.) Preparing to unpack .../perl_5.38.2-3.2+b2_amd64.deb ... Unpacking perl (5.38.2-3.2+b2) over (5.36.0-7+deb12u1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libsasl2-modules-db:amd64 depends on libdb5.3. libperl5.36:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47229 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47229 files and directories currently installed.) Removing libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm6t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47223 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1+b1) ... dpkg: libgdbm-compat4:amd64: dependency problems, but removing anyway as you requested: libperl5.36:amd64 depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47231 files and directories currently installed.) Removing libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47225 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../libperl5.38t64_5.38.2-3.2+b2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Preparing to unpack .../perl-base_5.38.2-3.2+b2_amd64.deb ... Unpacking perl-base (5.38.2-3.2+b2) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-3.2+b2) ... (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 ... 47758 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5.1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5.1) over (1.0.8-5+b1) ... Setting up libbz2-1.0:amd64 (1.0.8-5.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47757 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47757 files and directories currently installed.) Preparing to unpack .../debconf_1.5.86_all.deb ... Unpacking debconf (1.5.86) over (1.5.82) ... Setting up debconf (1.5.86) ... Installing new version of config file /etc/debconf.conf ... (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 ... 47756 files and directories currently installed.) Preparing to unpack .../tzdata_2024a-2_all.deb ... Unpacking tzdata (2024a-2) over (2024a-0+deb12u1) ... Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.6-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.1+really5.4.5-1_amd64.deb ... Unpacking liblzma5:amd64 (5.6.1+really5.4.5-1) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.6.1+really5.4.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.45.2-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.2-1) over (3.40.1-2) ... Preparing to unpack .../libcap2_1%3a2.66-5_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-5) over (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-5) ... (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 ... 46972 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.47-3_amd64.deb ... Unpacking libgpg-error0:amd64 (1.47-3) over (1.46-1) ... Setting up libgpg-error0:amd64 (1.47-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-2_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-2) over (1.9.4-1) ... Setting up liblz4-1:amd64 (1.9.4-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libsystemd0_255.4-1+b1_amd64.deb ... Unpacking libsystemd0:amd64 (255.4-1+b1) over (252.22-1~deb12u1) ... Setting up libsystemd0:amd64 (255.4-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46973 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46973 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-2) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.4-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-2.1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-6_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam0g:amd64 (1.5.3-6) ... (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 ... 46971 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4+b1) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2+b2_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2+b2) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-2+b2) ... (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 ... 46973 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-6_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-6) ... (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 ... 46972 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-6_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-6) over (1.5.2-6+deb12u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-6) ... Installing new version of config file /etc/security/namespace.init ... (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 ... 46969 files and directories currently installed.) Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... Preparing to unpack .../libldap-2.5-0_2.5.16+dfsg-2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.16+dfsg-2) over (2.5.13+dfsg-5) ... Selecting previously unselected package gcc-14-base:amd64. Preparing to unpack .../gcc-14-base_14-20240330-1_amd64.deb ... Unpacking gcc-14-base:amd64 (14-20240330-1) ... Setting up gcc-14-base:amd64 (14-20240330-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14-20240330-1_amd64.deb ... Unpacking libgcc-s1:amd64 (14-20240330-1) over (12.2.0-14) ... Setting up libgcc-s1:amd64 (14-20240330-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libstdc++6_14-20240330-1_amd64.deb ... Unpacking libstdc++6:amd64 (14-20240330-1) over (12.2.0-14) ... Setting up libstdc++6:amd64 (14-20240330-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46972 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2+b1) over (2:6.2.1+dfsg1-1.1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-2+b1) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.7~). (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 ... 46973 files and directories currently installed.) Removing libnettle8:amd64 (3.8.1-2) ... Selecting previously unselected package libnettle8t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46965 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2_amd64.deb ... Unpacking libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libnettle8t64:amd64 (3.9.1-2.2) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (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 ... 46974 files and directories currently installed.) Removing libhogweed6:amd64 (3.8.1-2) ... Selecting previously unselected package libhogweed6t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46968 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46975 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-4) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.3-4) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (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 ... 46975 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.9-2+deb12u2) ... Selecting previously unselected package libgnutls30t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46946 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.5-1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.5-1) ... Setting up libgnutls30t64:amd64 (3.8.5-1) ... dpkg: libapt-pkg6.0:amd64: dependency problems, but removing anyway as you requested: apt depends on libapt-pkg6.0 (>= 2.6.1). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46975 files and directories currently installed.) Removing libapt-pkg6.0:amd64 (2.6.1) ... Selecting previously unselected package libapt-pkg6.0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46926 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.14_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.7.14) ... Setting up libapt-pkg6.0t64:amd64 (2.7.14) ... (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 ... 46976 files and directories currently installed.) Preparing to unpack .../libudev1_255.4-1+b1_amd64.deb ... Unpacking libudev1:amd64 (255.4-1+b1) over (252.22-1~deb12u1) ... Setting up libudev1:amd64 (255.4-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46977 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2+b1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.2-2+b1) over (0.8.1-1) ... Setting up libxxhash0:amd64 (0.8.2-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46978 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271+b3_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271+b3) over (0.270) ... Setting up libdebconfclient0:amd64 (0.271+b3) ... (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 ... 46979 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.6.1) ... Setting up base-passwd (3.6.3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46979 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1) ... Setting up libsemanage-common (3.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46979 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46979 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b3_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b3) over (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.5-1+b3) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 48694 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.3-11_amd64.deb ... Unpacking util-linux-extra (2.39.3-11) over (2.38.1-5+b1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty Setting up util-linux-extra (2.39.3-11) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 48699 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-7_amd64.deb ... Unpacking sysvinit-utils (3.08-7) over (3.06-4) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-7) ... Selecting previously unselected package gcc-13-base:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 48699 files and directories currently installed.) Preparing to unpack .../00-gcc-13-base_13.2.0-23_amd64.deb ... Unpacking gcc-13-base:amd64 (13.2.0-23) ... Preparing to unpack .../01-libitm1_14-20240330-1_amd64.deb ... Unpacking libitm1:amd64 (14-20240330-1) over (12.2.0-14) ... Preparing to unpack .../02-libatomic1_14-20240330-1_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.0-2.4) ... Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up libext2fs2t64:amd64 (1.47.0-2.4) ... (Reading database ... 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Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:amd64 (3.12.2-5) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up gcc (4:13.2.0-7) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up libpython3.11-dev:amd64 (3.11.8-3+b3) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.4-3) ... Setting up python3.12-dev (3.12.2-5) ... Setting up libnsl-dev:amd64 (1.3.0-3+b2) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lib2to3 (3.12.2-3) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.2-3) ... python3.12: can't get files for byte-compilation Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up g++-13 (13.2.0-23) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3.11-dev (3.11.8-3+b3) ... Setting up python3-ply (3.11-6) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-networkx (2.8.8-2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-fs (2.4.16-3) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libpython3-all-dev:amd64 (3.11.8-1) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-numpy (1:1.26.4+ds-6) ... Setting up g++ (4:13.2.0-7) ... Setting up python3-contourpy (1.0.7-3) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pomegranate (0.14.8-4) ... Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-7) ... Setting up python3-sklearn-lib:amd64 (1.4.1.post1+dfsg-1) ... Setting up python3-pandas (2.1.4+dfsg-7) ... Setting up python3-sklearn (1.4.1.post1+dfsg-1) ... Setting up python3-pythran (0.15.0+ds-2) ... Setting up python3-pyfaidx (0.8.1.1-1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Processing triggers for sgml-base (1.31) ... Processing triggers for debianutils (5.17) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Processing triggers for mailcap (3.70+nmu1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Processing triggers for libc-bin (2.37-15.1) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libcairo2:amd64 (1.18.0-3) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-cairo (1.25.1-2) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-tk:amd64 (3.12.2-3) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up r-base-core (4.3.3-3+b1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Setting up python3-reportlab (4.1.0-4) ... Setting up python3-biopython (1.83+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b2) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up r-bioc-dnacopy (1.76.0-1) ... Setting up cnvkit (0.9.10-2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for libc-bin (2.37-15.1) ... 5m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-yf', 'dist-upgrade'] 5m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m12.9s DUMP: 9d2a1fd24989eb69187f2e1f09c7030b - 5m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 5m13.2s DUMP: Package: cnvkit Version: 0.9.10-2 Installed-Size: 94731 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description-en: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Homepage: https://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.10-2_all.deb Size: 19501620 MD5sum: 34bc5101407f83474714510d690c42f5 SHA256: bf1fd75c757a204fb8123b69285b16b389dfc0c840d3941227ff8c7f89a602e3 5m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 5m13.2s INFO: apt-cache knows about the following packages: cnvkit 5m13.2s INFO: Running scripts pre_install 5m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_database-server'] 5m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_database-server'] 5m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_exceptions'] 5m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_exceptions'] 5m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_extras'] 5m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_extras'] 5m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture'] 5m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture'] 5m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy'] 5m13.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy'] 5m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy', 'cnvkit'] 5m13.4s DUMP: cnvkit: Installed: 0.9.10-2 Candidate: 0.9.10-2 Version table: *** 0.9.10-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 5m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy', 'cnvkit'] 5m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', 'install', 'cnvkit'] 5m14.1s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.10-2). The following packages were automatically installed and are no longer required: libboost-dev libboost1.83-dev libglib2.0-0 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36 libpython3-all-dev libpython3.12-dev libpython3.12t64 libtirpc-dev libxsimd-dev perl-modules-5.36 python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev xtl-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', 'install', 'cnvkit'] 5m14.1s INFO: Running scripts post_install 5m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_install_exceptions'] 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_install_exceptions'] 5m14.1s INFO: Running scripts post_distupgrade 5m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_exceptions'] 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_exceptions'] 5m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_zz_backports'] 5m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_distupgrade_zz_backports'] 5m14.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 5m16.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 5m16.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 5m18.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 5m18.7s INFO: Running scripts pre_install 5m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_database-server'] 5m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_database-server'] 5m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_exceptions'] 5m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_exceptions'] 5m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_extras'] 5m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_extras'] 5m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture'] 5m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture'] 5m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy'] 5m18.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy'] 5m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy', 'cnvkit'] 5m18.9s DUMP: cnvkit: Installed: 0.9.10-2 Candidate: 0.9.10-2 Version table: *** 0.9.10-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 5m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-cache', 'policy', 'cnvkit'] 5m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', 'install', 'cnvkit=0.9.10-2'] 5m19.5s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.10-2). The following packages were automatically installed and are no longer required: libboost-dev libboost1.83-dev libglib2.0-0 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36 libpython3-all-dev libpython3.12-dev libpython3.12t64 libtirpc-dev libxsimd-dev perl-modules-5.36 python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev xtl-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', 'install', 'cnvkit=0.9.10-2'] 5m19.5s INFO: Running scripts post_install 5m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_install_exceptions'] 5m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_install_exceptions'] 5m19.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 5m22.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 5m22.1s INFO: /bin converted to /usr/bin by /usr merge 5m22.1s INFO: /lib converted to /usr/lib by /usr merge 5m22.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 5m22.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 5m22.1s INFO: /sbin converted to /usr/sbin by /usr merge 5m25.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', '-ac', '--ignore-obsolete'] 5m32.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', '-ac', '--ignore-obsolete'] 5m32.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 5m32.1s DUMP: 0.15.6 5m32.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 5m32.1s INFO: Running adequate version 0.15.6 now. 5m32.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'cnvkit'] 5m32.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'cnvkit'] 5m32.3s INFO: Running scripts pre_remove 5m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 5m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 5m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 5m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 5m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 5m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 5m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_exceptions'] 5m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/pre_remove_exceptions'] 5m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 5m41.4s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.14 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed binutils binutils 2.42-4 install ok installed binutils-common:amd64 binutils-common 2.42-4 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.42-4 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.39.3-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed cnvkit cnvkit 0.9.10-2 install ok installed coreutils coreutils 9.4-3.1 install ok installed cpp cpp 4:13.2.0-7 install ok installed cpp-12 cpp-12 12.3.0-17 install ok installed cpp-13 cpp-13 13.2.0-23 install ok installed cpp-13-x86-64-linux-gnu cpp-13-x86-64-linux-gnu 13.2.0-23 install ok installed cpp-x86-64-linux-gnu cpp-x86-64-linux-gnu 4:13.2.0-7 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.0~RC4-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed g++ g++ 4:13.2.0-7 install ok installed g++-12 g++-12 12.3.0-17 install ok installed g++-13 g++-13 13.2.0-23 install ok installed g++-13-x86-64-linux-gnu g++-13-x86-64-linux-gnu 13.2.0-23 install ok installed g++-x86-64-linux-gnu g++-x86-64-linux-gnu 4:13.2.0-7 install ok installed gcc gcc 4:13.2.0-7 install ok installed gcc-12 gcc-12 12.3.0-17 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-17 install ok installed gcc-13 gcc-13 13.2.0-23 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-23 install ok installed gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu 13.2.0-23 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gcc-x86-64-linux-gnu gcc-x86-64-linux-gnu 4:13.2.0-7 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libasan8:amd64 libasan8 14-20240330-1 install ok installed libatomic1:amd64 libatomic1 14-20240330-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libbinutils:amd64 libbinutils 2.42-4 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-11 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-2.1+b1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc-dev-bin libc-dev-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libc6-dev:amd64 libc6-dev 2.37-15.1 install ok installed libcairo2:amd64 libcairo2 1.18.0-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcc1-0:amd64 libcc1-0 14-20240330-1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.42-4 install ok installed libctf0:amd64 libctf0 2.42-4 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.7.1-2 install ok installed libcurl4t64:amd64 libcurl4t64 8.7.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b3 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.3.0-17 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-23 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1+b1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1+b1 install ok installed libgfortran5:amd64 libgfortran5 14-20240330-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-6 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-1 install ok installed libgomp1:amd64 libgomp1 14-20240330-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgprofng0:amd64 libgprofng0 2.42-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6+b1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhts3t64:amd64 libhts3t64 1.19+ds-1.1+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libhwasan0:amd64 libhwasan0 14-20240330-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1 install ok installed libisl23:amd64 libisl23 0.26-3+b2 install ok installed libitm1:amd64 libitm1 14-20240330-1 install ok installed libjansson4:amd64 libjansson4 2.14-2+b2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 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 7.2.6-6 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblsan0:amd64 liblsan0 14-20240330-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-11 install ok installed libmpc3:amd64 libmpc3 1.3.1-1+b2 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.61.0-1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3+b2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.26+ds-1 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.26+ds-1 install ok installed libopenblas0:amd64 libopenblas0 0.3.26+ds-1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.26+ds-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.1+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.1+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.1+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 10.42-4+b1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2+b2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-4 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.11.8-1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.8-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.8-3+b3 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-3+b3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-3+b3 install ok installed libpython3.11t64:amd64 libpython3.11t64 3.11.8-3+b3 install ok installed libpython3.12-dev:amd64 libpython3.12-dev 3.12.2-5 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.2-5 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.2-5 install ok installed libpython3.12t64:amd64 libpython3.12t64 3.12.2-5 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b1 install ok installed libquadmath0:amd64 libquadmath0 14-20240330-1 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsframe1:amd64 libsframe1 2.42-4 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4+b1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.2-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b2 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.3.0-17 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-23 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.2 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.2 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.2 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtsan2:amd64 libtsan2 14-20240330-1 install ok installed libubsan1:amd64 libubsan1 14-20240330-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-11 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.3.2-0.4+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.3.2-0.4+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 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+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxsimd-dev:amd64 libxsimd-dev 12.1.1-3 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 libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev linux-libc-dev 6.7.9-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.39.3-11 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.2.1-3 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2+b2 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed procps procps 2:4.0.4-4 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-1 install ok installed python3 python3 3.11.8-1 install ok installed python3-all python3-all 3.11.8-1 install ok installed python3-all-dev python3-all-dev 3.11.8-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 23.2.0-2 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-biopython python3-biopython 1.83+dfsg1-1 install ok installed python3-brotli python3-brotli 1.1.0-2+b3 install ok installed python3-cairo python3-cairo 1.25.1-2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-contourpy python3-contourpy 1.0.7-3 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-2 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-dev python3-dev 3.11.8-1 install ok installed python3-distutils python3-distutils 3.12.2-3 install ok installed python3-fonttools python3-fonttools 4.46.0-1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-fs python3-fs 2.4.16-3 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-importlib-metadata python3-importlib-metadata 4.12.0-1 install ok installed python3-joblib python3-joblib 1.3.2-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.4-3 install ok installed python3-lib2to3 python3-lib2to3 3.12.2-3 install ok installed python3-lxml:amd64 python3-lxml 5.2.1-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b3 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1+b2 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3-more-itertools python3-more-itertools 10.2.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-networkx python3-networkx 2.8.8-2 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-6 install ok installed python3-packaging python3-packaging 24.0-1 install ok installed python3-pandas python3-pandas 2.1.4+dfsg-7 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.1.4+dfsg-7 install ok installed python3-pil:amd64 python3-pil 10.3.0-2 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.3.0-2 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-ply python3-ply 3.11-6 install ok installed python3-pomegranate python3-pomegranate 0.14.8-4 install ok installed python3-pyfaidx python3-pyfaidx 0.8.1.1-1 install ok installed python3-pyparsing python3-pyparsing 3.1.1-1 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b2 install ok installed python3-pythran python3-pythran 0.15.0+ds-2 install ok installed python3-reportlab python3-reportlab 4.1.0-4 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.11.4-6 install ok installed python3-setuptools python3-setuptools 68.1.2-2 install ok installed python3-six python3-six 1.16.0-6 install ok installed python3-sklearn python3-sklearn 1.4.1.post1+dfsg-1 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 1.4.1.post1+dfsg-1 install ok installed python3-sympy python3-sympy 1.12-7 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.12.2-3 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3-yaml python3-yaml 6.0.1-2 install ok installed python3-zipp python3-zipp 1.0.0-6 install ok installed python3.11 python3.11 3.11.8-3+b3 install ok installed python3.11-dev python3.11-dev 3.11.8-3+b3 install ok installed python3.11-minimal python3.11-minimal 3.11.8-3+b3 install ok installed python3.12 python3.12 3.12.2-5 install ok installed python3.12-dev python3.12-dev 3.12.2-5 install ok installed python3.12-minimal python3.12-minimal 3.12.2-5 install ok installed r-base-core r-base-core 4.3.3-3+b1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.48.1-2 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.76.0-1 install ok installed readline-common readline-common 8.2-4 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024a-2 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-11 install ok installed util-linux-extra util-linux-extra 2.39.3-11 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 0.19 install ok installed xtl-dev xtl-dev 0.7.5-3 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3.1 5m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 5m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'binutils-', 'binutils-common:amd64-', 'binutils-x86-64-linux-gnu-', 'blt-', 'ca-certificates-', 'cpp-', 'cpp-12-', 'cpp-13-', 'cpp-13-x86-64-linux-gnu-', 'cpp-x86-64-linux-gnu-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'fonts-lyx-', 'fonts-urw-base35-', 'g++-', 'g++-12-', 'g++-13-', 'g++-13-x86-64-linux-gnu-', 'g++-x86-64-linux-gnu-', 'gcc-', 'gcc-12-', 'gcc-13-', 'gcc-13-base:amd64-', 'gcc-13-x86-64-linux-gnu-', 'gcc-x86-64-linux-gnu-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libbinutils:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost1.83-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-', 'libcurl3t64-gnutls:amd64-', 'libcurl4t64:amd64-', 'libdatrie1:amd64-', 'libdb5.3t64:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libexpat1-dev:amd64-', 'libfontconfig1:amd64-', 'libfontenc1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgcc-12-dev:amd64-', 'libgcc-13-dev:amd64-', 'libgdbm-compat4t64:amd64-', 'libgdbm6t64:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgprofng0:amd64-', 'libgraphite2-3:amd64-', 'libgssapi-krb5-2:amd64-', 'libharfbuzz0b:amd64-', 'libhts3t64:amd64-', 'libhtscodecs2:amd64-', 'libhwasan0: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-', 'libperl5.38t64:amd64-', 'libpixman-1-0:amd64-', 'libpng16-16t64:amd64-', 'libproc2-0:amd64-', 'libpsl5t64:amd64-', 'libpython3-all-dev:amd64-', 'libpython3-dev:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-dev:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.11t64:amd64-', 'libpython3.12-dev:amd64-', 'libpython3.12-minimal:amd64-', 'libpython3.12-stdlib:amd64-', 'libpython3.12t64:amd64-', 'libqhull-r8.0:amd64-', 'libquadmath0:amd64-', 'libraqm0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsframe1:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libsqlite3-0:amd64-', 'libssh2-1t64:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff6:amd64-', 'libtirpc-common-', 'libtirpc-dev:amd64-', 'libtirpc3t64: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-', 'libxt6t64:amd64-', 'libyaml-0-2:amd64-', 'linux-libc-dev-', 'mailcap-', 'media-types-', 'mime-support-', 'netbase-', 'openssl-', 'perl-', 'perl-modules-5.36-', 'perl-modules-5.38-', 'procps-', 'python-matplotlib-data-', 'python3-', 'python3-all-', 'python3-all-dev-', 'python3-appdirs-', 'python3-attr-', 'python3-beniget-', 'python3-biopython-', 'python3-brotli-', 'python3-cairo-', 'python3-chardet-', 'python3-contourpy-', 'python3-cycler-', 'python3-dateutil-', 'python3-decorator-', 'python3-dev-', 'python3-distutils-', 'python3-fonttools-', 'python3-freetype-', 'python3-fs-', 'python3-gast-', 'python3-importlib-metadata-', 'python3-joblib-', 'python3-kiwisolver-', 'python3-lib2to3-', 'python3-lxml:amd64-', 'python3-lz4-', 'python3-matplotlib-', 'python3-minimal-', 'python3-more-itertools-', '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-reportlab-', 'python3-rlpycairo-', 'python3-scipy-', 'python3-setuptools-', 'python3-six-', 'python3-sklearn-', 'python3-sklearn-lib:amd64-', 'python3-sympy-', 'python3-threadpoolctl-', 'python3-tk:amd64-', 'python3-tz-', 'python3-ufolib2-', 'python3-yaml-', 'python3-zipp-', 'python3.11-', 'python3.11-dev-', 'python3.11-minimal-', 'python3.12-', 'python3.12-dev-', 'python3.12-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-', 'xtl-dev-', 'zip-', 'zlib1g-dev:amd64-', 'cnvkit-'] 6m40.3s 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 cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-12 g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-12 gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdb5.3t64 libdeflate0 libexpat1 libexpat1-dev libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0 libglib2.0-0t64 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 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 libperl5.38t64 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.11t64 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsframe1 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libstdc++-12-dev libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3t64 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 libxt6t64 libyaml-0-2 linux-libc-dev mailcap media-types mime-support netbase openssl perl perl-modules-5.36 perl-modules-5.38 procps python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-freetype python3-fs python3-gast python3-importlib-metadata python3-joblib python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-pythran python3-reportlab python3-rlpycairo python3-scipy python3-setuptools python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-yaml python3-zipp python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-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 xtl-dev zip zlib1g-dev The following NEW packages will be installed: libdb5.3 0 upgraded, 1 newly installed, 262 to remove and 0 not upgraded. Need to get 697 kB of archives. After this operation, 1746 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 697 kB in 0s (7203 kB/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 ... 53760 files and directories currently installed.) Removing python3-pythran (0.15.0+ds-2) ... Removing g++ (4:13.2.0-7) ... Removing gcc (4:13.2.0-7) ... Removing g++-12 (12.3.0-17) ... Removing gcc-12 (12.3.0-17) ... Removing g++-x86-64-linux-gnu (4:13.2.0-7) ... Removing gcc-x86-64-linux-gnu (4:13.2.0-7) ... Removing g++-13 (13.2.0-23) ... Removing g++-13-x86-64-linux-gnu (13.2.0-23) ... Removing cnvkit (0.9.10-2) ... Removing python3-biopython (1.83+dfsg1-1) ... Removing python3-reportlab (4.1.0-4) ... Removing python3-matplotlib (3.6.3-1+b2) ... Removing python3-pil.imagetk:amd64 (10.3.0-2) ... Removing python3-pil:amd64 (10.3.0-2) ... Removing python3-tk:amd64 (3.12.2-3) ... Removing blt (2.5.3+dfsg-7) ... Removing r-bioc-dnacopy (1.76.0-1) ... Removing r-bioc-biocgenerics (0.48.1-2) ... Removing r-base-core (4.3.3-3+b1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp (4:13.2.0-7) ... Removing cpp-12 (12.3.0-17) ... Removing cpp-13 (13.2.0-23) ... Removing cpp-x86-64-linux-gnu (4:13.2.0-7) ... Removing libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.1+ds-1) ... Removing fontconfig (2.15.0-1.1) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.25.1-2) ... Removing libcairo2:amd64 (1.18.0-3) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing python-matplotlib-data (3.6.3-1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.0~RC4-1) ... Removing fonts-urw-base35 (20200910-8) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-2.1+b1) ... Removing libstdc++-13-dev:amd64 (13.2.0-23) ... Removing libstdc++-12-dev:amd64 (12.3.0-17) ... Removing libgcc-12-dev:amd64 (12.3.0-17) ... Removing python3-sklearn (1.4.1.post1+dfsg-1) ... Removing python3-pomegranate (0.14.8-4) ... Removing python3-sklearn-lib:amd64 (1.4.1.post1+dfsg-1) ... Removing python3-pandas (2.1.4+dfsg-7) ... Removing python3-pandas-lib:amd64 (2.1.4+dfsg-7) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing xfonts-utils (1:7.7+6) ... Removing libraqm0:amd64 (0.10.1-1+b1) ... Removing libcurl4t64:amd64 (8.7.1-2) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... 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 python3-all-dev (3.11.8-1) ... Removing python3.12-dev (3.12.2-5) ... Removing libpython3-all-dev:amd64 (3.11.8-1) ... Removing libpython3.12-dev:amd64 (3.12.2-5) ... Removing python3-dev (3.11.8-1) ... Removing python3.11-dev (3.11.8-3+b3) ... Removing python3-pysam (0.22.0+ds-1+b2) ... Removing libhts3t64:amd64 (1.19+ds-1.1+b1) ... Removing libcurl3t64-gnutls:amd64 (8.7.1-2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libpython3.12t64:amd64 (3.12.2-5) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing python3-yaml (6.0.1-2) ... Removing python3-setuptools (68.1.2-2) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libfontenc1:amd64 (1:1.1.8-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.38.2-3.2+b2) ... Removing libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Removing libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Removing libgdbm6t64:amd64 (1.23-5.1+b1) ... Removing libopenblas-dev:amd64 (0.3.26+ds-1) ... Removing libopenblas-pthread-dev:amd64 (0.3.26+ds-1) ... Removing libopenblas0:amd64 (0.3.26+ds-1) ... Removing libglib2.0-0:amd64 (2.78.4-6) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libglib2.0-0t64:amd64 (2.78.4-6) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libnsl-dev:amd64 (1.3.0-3+b2) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.2) ... Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.2) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libjs-sphinxdoc (7.2.6-6) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing libkrb5-3:amd64 (1.20.1-6+b1) ... Removing libk5crypto3:amd64 (1.20.1-6+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-6+b1) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing python3-joblib (1.3.2-2) ... Removing procps (2:4.0.4-4) ... Removing libnghttp2-14:amd64 (1.61.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b3) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libproc2-0:amd64 (2:4.0.4-4) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libpython3-dev:amd64 (3.11.8-1) ... Removing libqhull-r8.0:amd64 (2020.2-6+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libwebpmux3:amd64 (1.3.2-0.4+b1) ... Removing libwebpdemux2:amd64 (1.3.2-0.4+b1) ... Removing libwebp7:amd64 (1.3.2-0.4+b1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.2) ... 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 libxsimd-dev:amd64 (12.1.1-3) ... Removing libyaml-0-2:amd64 (0.2.5-1) ... Removing openssl (3.2.1-3) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing perl-modules-5.38 (5.38.2-3.2) ... Removing python3-beniget (0.4.1-3) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-contourpy (1.0.7-3) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-2) ... Removing python3-freetype (2.4.0-1) ... Removing python3-gast (0.5.2-2) ... Removing python3-pyfaidx (0.8.1.1-1) ... Removing python3-importlib-metadata (4.12.0-1) ... Removing python3-kiwisolver (1.4.4-3) ... Removing python3-zipp (1.0.0-6) ... Removing python3-more-itertools (10.2.0-1) ... Removing python3-networkx (2.8.8-2) ... Removing python3-packaging (24.0-1) ... Removing python3-ply (3.11-6) ... Removing python3-pyparsing (3.1.1-1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing unzip (6.0-28) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... 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 xtl-dev (0.7.5-3) ... Removing zip (3.0-13) ... Removing gcc-13 (13.2.0-23) ... Removing binutils (2.42-4) ... Removing gcc-13-x86-64-linux-gnu (13.2.0-23) ... Removing binutils-x86-64-linux-gnu (2.42-4) ... Removing libgprofng0:amd64 (2.42-4) ... Removing libctf0:amd64 (2.42-4) ... Removing libbinutils:amd64 (2.42-4) ... Removing binutils-common:amd64 (2.42-4) ... Removing cpp-13-x86-64-linux-gnu (13.2.0-23) ... Removing libgcc-13-dev:amd64 (13.2.0-23) ... Removing gcc-13-base:amd64 (13.2.0-23) ... Removing libasan8:amd64 (14-20240330-1) ... Removing libatomic1:amd64 (14-20240330-1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b3) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.12.2-1) ... Removing libpython3.11-dev:amd64 (3.11.8-3+b3) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Removing libexpat1-dev:amd64 (2.6.2-1) ... Removing libc6-dev:amd64 (2.37-15.1) ... Removing libc-dev-bin (2.37-15.1) ... Removing libcc1-0:amd64 (14-20240330-1) ... Removing libcrypt-dev:amd64 (1:4.4.36-4) ... Removing libctf-nobfd0:amd64 (2.42-4) ... Removing libgomp1:amd64 (14-20240330-1) ... Removing libhwasan0:amd64 (14-20240330-1) ... Removing libisl23:amd64 (0.26-3+b2) ... Removing libitm1:amd64 (14-20240330-1) ... Removing libjansson4:amd64 (2.14-2+b2) ... Removing liblsan0:amd64 (14-20240330-1) ... Removing libmpc3:amd64 (1.3.1-1+b2) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libpython3.11t64:amd64 (3.11.8-3+b3) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing libquadmath0:amd64 (14-20240330-1) ... Removing libsframe1:amd64 (2.42-4) ... Removing libtsan2:amd64 (14-20240330-1) ... Removing libubsan1:amd64 (14-20240330-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing linux-libc-dev (6.7.9-2) ... Removing rpcsvc-proto (1.4.3-1) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... Removing python3-attr (23.2.0-2) ... Removing python3-fonttools (4.46.0-1) ... Removing python3-all (3.11.8-1) ... Removing python3.12 (3.12.2-5) ... Removing libpython3.12-stdlib:amd64 (3.12.2-5) ... Removing python3-distutils (3.12.2-3) ... Removing python3.12-minimal (3.12.2-5) ... Removing python3-lxml:amd64 (5.2.1-1) ... Removing libxslt1.1:amd64 (1.1.35-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libpython3.12-minimal:amd64 (3.12.2-5) ... Removing python3-fs (2.4.16-3) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-brotli (1.1.0-2+b3) ... Removing python3-lib2to3 (3.12.2-3) ... Removing python3-lz4 (4.0.2+dfsg-1+b3) ... Removing python3-sympy (1.12-7) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-six (1.16.0-6) ... Removing python3-tz (2024.1-2) ... Removing unicode-data (15.1.0-1) ... Removing python3-scipy (1.11.4-6) ... Removing python3-numpy (1:1.26.4+ds-6) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Removing libopenblas0-pthread:amd64 (0.3.26+ds-1) ... Removing libgfortran5:amd64 (14-20240330-1) ... Removing python3-decorator (5.1.1-5) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.8-3+b3) ... Removing python3-minimal (3.11.8-1) ... Removing python3.11-minimal (3.11.8-3+b3) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-3+b3) ... find: '/usr/lib/python3': No such file or directory Removing libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpython3.11-minimal:amd64 (3.11.8-3+b3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.45.2-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-4) ... Selecting previously unselected package libdb5.3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5412 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 6m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'binutils-', 'binutils-common:amd64-', 'binutils-x86-64-linux-gnu-', 'blt-', 'ca-certificates-', 'cpp-', 'cpp-12-', 'cpp-13-', 'cpp-13-x86-64-linux-gnu-', 'cpp-x86-64-linux-gnu-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'fonts-lyx-', 'fonts-urw-base35-', 'g++-', 'g++-12-', 'g++-13-', 'g++-13-x86-64-linux-gnu-', 'g++-x86-64-linux-gnu-', 'gcc-', 'gcc-12-', 'gcc-13-', 'gcc-13-base:amd64-', 'gcc-13-x86-64-linux-gnu-', 'gcc-x86-64-linux-gnu-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libbinutils:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost1.83-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-', 'libcurl3t64-gnutls:amd64-', 'libcurl4t64:amd64-', 'libdatrie1:amd64-', 'libdb5.3t64:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libexpat1-dev:amd64-', 'libfontconfig1:amd64-', 'libfontenc1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgcc-12-dev:amd64-', 'libgcc-13-dev:amd64-', 'libgdbm-compat4t64:amd64-', 'libgdbm6t64:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgprofng0:amd64-', 'libgraphite2-3:amd64-', 'libgssapi-krb5-2:amd64-', 'libharfbuzz0b:amd64-', 'libhts3t64:amd64-', 'libhtscodecs2:amd64-', 'libhwasan0: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-', 'libperl5.38t64:amd64-', 'libpixman-1-0:amd64-', 'libpng16-16t64:amd64-', 'libproc2-0:amd64-', 'libpsl5t64:amd64-', 'libpython3-all-dev:amd64-', 'libpython3-dev:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-dev:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.11t64:amd64-', 'libpython3.12-dev:amd64-', 'libpython3.12-minimal:amd64-', 'libpython3.12-stdlib:amd64-', 'libpython3.12t64:amd64-', 'libqhull-r8.0:amd64-', 'libquadmath0:amd64-', 'libraqm0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsframe1:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libsqlite3-0:amd64-', 'libssh2-1t64:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff6:amd64-', 'libtirpc-common-', 'libtirpc-dev:amd64-', 'libtirpc3t64: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-', 'libxt6t64:amd64-', 'libyaml-0-2:amd64-', 'linux-libc-dev-', 'mailcap-', 'media-types-', 'mime-support-', 'netbase-', 'openssl-', 'perl-', 'perl-modules-5.36-', 'perl-modules-5.38-', 'procps-', 'python-matplotlib-data-', 'python3-', 'python3-all-', 'python3-all-dev-', 'python3-appdirs-', 'python3-attr-', 'python3-beniget-', 'python3-biopython-', 'python3-brotli-', 'python3-cairo-', 'python3-chardet-', 'python3-contourpy-', 'python3-cycler-', 'python3-dateutil-', 'python3-decorator-', 'python3-dev-', 'python3-distutils-', 'python3-fonttools-', 'python3-freetype-', 'python3-fs-', 'python3-gast-', 'python3-importlib-metadata-', 'python3-joblib-', 'python3-kiwisolver-', 'python3-lib2to3-', 'python3-lxml:amd64-', 'python3-lz4-', 'python3-matplotlib-', 'python3-minimal-', 'python3-more-itertools-', '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-reportlab-', 'python3-rlpycairo-', 'python3-scipy-', 'python3-setuptools-', 'python3-six-', 'python3-sklearn-', 'python3-sklearn-lib:amd64-', 'python3-sympy-', 'python3-threadpoolctl-', 'python3-tk:amd64-', 'python3-tz-', 'python3-ufolib2-', 'python3-yaml-', 'python3-zipp-', 'python3.11-', 'python3.11-dev-', 'python3.11-minimal-', 'python3.12-', 'python3.12-dev-', 'python3.12-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-', 'xtl-dev-', 'zip-', 'zlib1g-dev:amd64-', 'cnvkit-'] 6m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1'] 6m41.6s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/697 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 5419 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... 6m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1'] 6m41.6s INFO: Running scripts post_remove 6m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_remove_exceptions'] 6m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_remove_exceptions'] 6m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-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', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhwasan0: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', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.11t64:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64: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', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'linux-libc-dev', 'mailcap', 'media-types', 'mime-support', 'netbase', 'openssl', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'procps', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gast', 'python3-importlib-metadata', 'python3-joblib', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', '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-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-yaml', 'python3-zipp', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-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', 'xtl-dev', 'zip', 'zlib1g-dev:amd64'] 6m42.6s DUMP: dpkg: warning: ignoring request to remove binutils which isn't installed (Reading database ... 5419 files and directories currently installed.) Purging configuration files for binutils-common:amd64 (2.42-4) ... 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 (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for cpp (4:13.2.0-7) ... dpkg: warning: ignoring request to remove cpp-12 which isn't installed dpkg: warning: ignoring request to remove cpp-13 which isn't installed dpkg: warning: ignoring request to remove cpp-13-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove cpp-x86-64-linux-gnu which isn't installed Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-12 which isn't installed dpkg: warning: ignoring request to remove g++-13 which isn't installed dpkg: warning: ignoring request to remove g++-13-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove g++-x86-64-linux-gnu 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 gcc-13 which isn't installed dpkg: warning: ignoring request to remove gcc-13-base which isn't installed dpkg: warning: ignoring request to remove gcc-13-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove gcc-x86-64-linux-gnu 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 libboost1.83-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 (1:4.4.36-4) ... 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 libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdb5.3t64 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 libgcc-13-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libglib2.0-0 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-6) ... 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 (1.20.1-6+b1) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 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 libperl5.38t64 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-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-dev which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-3+b3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.11t64 which isn't installed dpkg: warning: ignoring request to remove libpython3.12-dev which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.2-5) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.12t64 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 Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsframe1 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-13-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 (1.3.4+ds-1.2) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.2) ... 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 libxt6t64 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 (10.1.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.2.1-3) ... Purging configuration files for perl (5.38.2-3.2+b2) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for procps (2:4.0.4-4) ... Purging configuration files for python-matplotlib-data (3.6.3-1) ... Purging configuration files for python3 (3.11.8-1) ... 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-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-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-freetype 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-importlib-metadata which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-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-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-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-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-sklearn which isn't installed dpkg: warning: ignoring request to remove python3-sklearn-lib which isn't installed Purging configuration files for python3-sympy (1.12-7) ... 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-zipp 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 (3.11.8-3+b3) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed dpkg: warning: ignoring request to remove python3.12-dev which isn't installed Purging configuration files for python3.12-minimal (3.12.2-5) ... Purging configuration files for r-base-core (4.3.3-3+b1) ... dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-dnacopy which isn't installed Purging configuration files for readline-common (8.2-4) ... dpkg: warning: ignoring request to remove 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: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.19) ... dpkg: warning: ignoring request to remove xtl-dev which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 6m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-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', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhwasan0: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', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.11t64:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64: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', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'linux-libc-dev', 'mailcap', 'media-types', 'mime-support', 'netbase', 'openssl', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'procps', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gast', 'python3-importlib-metadata', 'python3-joblib', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', '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-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3-yaml', 'python3-zipp', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-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', 'xtl-dev', 'zip', 'zlib1g-dev:amd64'] 6m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--purge', 'cnvkit'] 6m42.6s DUMP: dpkg: warning: ignoring request to remove cnvkit which isn't installed 6m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--purge', 'cnvkit'] 6m42.6s INFO: Running scripts post_purge 6m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_purge_exceptions'] 6m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_purge_exceptions'] 6m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--purge', '--pending'] 6m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--purge', '--pending'] 6m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--remove', '--pending'] 6m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg', '--remove', '--pending'] 6m42.7s INFO: Running scripts post_test 6m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_test_exceptions'] 6m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'tmp/scripts/post_test_exceptions'] 6m42.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 6m43.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 6m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg-divert', '--list'] 6m43.0s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 6m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'dpkg-divert', '--list'] 6m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', 'clean'] 6m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl1e1234q', 'apt-get', 'clean'] 6m43.1s DEBUG: Recording chroot state 6m43.7s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 6m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/shm'] 6m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/shm'] 6m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/console'] 6m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/console'] 6m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/ptmx'] 6m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/ptmx'] 6m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/pts'] 6m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/dev/pts'] 6m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/proc'] 6m44.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl1e1234q/proc'] 6m44.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 6m44.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl1e1234q'] 6m44.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpl1e1234q 6m44.1s INFO: PASS: Upgrading between Debian distributions. 6m44.1s INFO: PASS: All tests. 6m44.1s INFO: piuparts run ends. ret=0 End: 2024-04-08 15:58:55 GMT