Start: 2024-08-21 06:21:42 GMT [bookworm] Package: python3-biopython Source: python-biopython (1.80+dfsg-4) Version: 1.80+dfsg-4+b1 Installed-Size: 11325 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libc6 (>= 2.14), python3-renderpm, python3-reportlab, w3c-sgml-lib Recommends: python-biopython-doc (= 1.80+dfsg-4), ncbi-blast+ (>= 2.10.1-3) Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle3, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise Breaks: cnvkit (<< 0.9.7-1~), ncbi-acc-download (<< 0.2.7-2~) Description: Python3 library for bioinformatics Homepage: https://biopython.org Description-md5: b0edcac4d61d56d664f586a477d26535 Section: python Priority: optional Filename: pool/main/p/python-biopython/python3-biopython_1.80+dfsg-4+b1_amd64.deb Size: 1593248 MD5sum: 87c665539ca8b339a1da0729e2afd5cf SHA256: 5888356eff82d5fd535ba4baff9f13dcadd7217fde56e9e1f805c253966923d8 [bookworm-next] Package: python3-biopython Source: python-biopython (1.80+dfsg-4) Version: 1.80+dfsg-4+b1 Installed-Size: 11325 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libc6 (>= 2.14), python3-renderpm, python3-reportlab, w3c-sgml-lib Recommends: python-biopython-doc (= 1.80+dfsg-4), ncbi-blast+ (>= 2.10.1-3) Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle3, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise Breaks: cnvkit (<< 0.9.7-1~), ncbi-acc-download (<< 0.2.7-2~) Description: Python3 library for bioinformatics Homepage: https://biopython.org Description-md5: b0edcac4d61d56d664f586a477d26535 Section: python Priority: optional Filename: pool/main/p/python-biopython/python3-biopython_1.80+dfsg-4+b1_amd64.deb Size: 1593248 MD5sum: 87c665539ca8b339a1da0729e2afd5cf SHA256: 5888356eff82d5fd535ba4baff9f13dcadd7217fde56e9e1f805c253966923d8 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt python3-biopython=1.80+dfsg-4+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201642~1.4.3-11-g36a88c35 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt python3-biopython=1.80+dfsg-4+b1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpw3b9j1j2 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpw3b9j1j2 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpw3b9j1j2/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'update'] 0m1.2s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'update'] 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.8s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.8s INFO: Running scripts post_setup 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_dummy_users'] 0m2.8s 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 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_dummy_users'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_forbid_home'] 0m2.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_forbid_home'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.8s 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' 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_minimize'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_minimize'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_zz_backports'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_setup_zz_backports'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.8s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s INFO: Running scripts pre_test 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_test_root_password'] 0m3.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_test_root_password'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'show', '--no-all-versions', 'python3-biopython'] 0m3.5s DUMP: Package: python3-biopython Source: python-biopython (1.80+dfsg-4) Version: 1.80+dfsg-4+b1 Installed-Size: 11325 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libc6 (>= 2.14), python3-renderpm, python3-reportlab, w3c-sgml-lib Recommends: python-biopython-doc (= 1.80+dfsg-4), ncbi-blast+ (>= 2.10.1-3) Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle3, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise Breaks: cnvkit (<< 0.9.7-1~), ncbi-acc-download (<< 0.2.7-2~) Description-en: Python3 library for bioinformatics The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. . It is a distributed collaborative effort to develop Python3 libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. The project works along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project. Description-md5: b0edcac4d61d56d664f586a477d26535 Homepage: https://biopython.org Section: python Priority: optional Filename: pool/main/p/python-biopython/python3-biopython_1.80+dfsg-4+b1_amd64.deb Size: 1593248 MD5sum: 87c665539ca8b339a1da0729e2afd5cf SHA256: 5888356eff82d5fd535ba4baff9f13dcadd7217fde56e9e1f805c253966923d8 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'show', '--no-all-versions', 'python3-biopython'] 0m3.5s INFO: apt-cache knows about the following packages: python3-biopython 0m3.5s INFO: Running scripts pre_install 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy'] 0m3.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy', 'python3-biopython'] 0m3.7s DUMP: python3-biopython: Installed: (none) Candidate: 1.80+dfsg-4+b1 Version table: 1.80+dfsg-4+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy', 'python3-biopython'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-y', 'install', 'python3-biopython'] 0m51.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gdbm-l10n low-memory-monitor krb5-doc krb5-user liblcms2-utils sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise gcc gfortran python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.11-venv python3.11-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-olefile ca-certificates The following NEW packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 47.0 MB of archives. After this operation, 176 MB of additional disk space will be used. 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amd64 1.0.8-2.1 [65.0 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:53 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amd64 1.15-1 [144 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+deb12u1 [472 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.0 MB in 0s (120 MB/s) Selecting previously unselected package perl-modules-5.36. 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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 ... 8957 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../02-libfontenc1_1%3a1.1.4-1_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.4-1) ... 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Unpacking libopenjp2-7:amd64 (2.5.0-2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../27-libraqm0_0.7.0-4.1_amd64.deb ... Unpacking libraqm0:amd64 (0.7.0-4.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../28-libwebp7_1.2.4-0.2+deb12u1_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../29-libtiff6_4.5.0-6+deb12u1_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-6+deb12u1) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../30-libwebpdemux2_1.2.4-0.2+deb12u1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../31-libwebpmux3_1.2.4-0.2+deb12u1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../32-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../33-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../34-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../35-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../36-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-renderpm:amd64. Preparing to unpack .../37-python3-renderpm_3.6.12-1+b1_amd64.deb ... Unpacking python3-renderpm:amd64 (3.6.12-1+b1) ... 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Unpacking python3-biopython (1.80+dfsg-4+b1) ... Setting up media-types (10.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libdeflate0:amd64 (1.14-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... 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 libjpeg62-turbo:amd64 (1:2.1.5-2) ... 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 libpng16-16:amd64 (1.6.39-2) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up libgdbm6:amd64 (1.23-3) ... 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 libxcb1:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up mailcap (3.70+nmu1) ... Setting up mime-support (3.66) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... 0m51.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-y', 'install', 'python3-biopython'] 0m51.9s INFO: Running scripts post_install 0m51.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_install_exceptions'] 0m51.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_install_exceptions'] 0m51.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 0m52.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 0m52.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpw3b9j1j2 to bookworm-next 0m52.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m52.6s INFO: Running scripts pre_distupgrade 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'update'] 0m53.9s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [170 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [103 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [90.8 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [51.3 kB] Fetched 608 kB in 1s (839 kB/s) Reading package lists... 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'update'] 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-yf', 'dist-upgrade'] 0m58.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 python3-numpy 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 11.4 MB of archives. After this operation, 1641 kB disk space will be freed. Get:1 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.13-1~deb12u2 [2023 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.4 MB in 0s (122 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 ... 12012 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12012 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-python3-numpy_1%3a1.24.2-1+deb12u1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1+deb12u1) over (1:1.24.2-1) ... Setting up libssl3:amd64 (3.0.13-1~deb12u2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up python3-numpy (1:1.24.2-1+deb12u1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m58.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-yf', 'dist-upgrade'] 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m59.5s DUMP: d4686440a37eea18c2739a6232b3b441 - 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'show', '--no-all-versions', 'python3-biopython'] 0m59.7s DUMP: Package: python3-biopython Source: python-biopython (1.80+dfsg-4) Version: 1.80+dfsg-4+b1 Installed-Size: 11325 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libc6 (>= 2.14), python3-renderpm, python3-reportlab, w3c-sgml-lib Recommends: python-biopython-doc (= 1.80+dfsg-4), ncbi-blast+ (>= 2.10.1-3) Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle3, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise Breaks: cnvkit (<< 0.9.7-1~), ncbi-acc-download (<< 0.2.7-2~) Description-en: Python3 library for bioinformatics The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. . It is a distributed collaborative effort to develop Python3 libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. The project works along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project. Description-md5: b0edcac4d61d56d664f586a477d26535 Homepage: https://biopython.org Section: python Priority: optional Filename: pool/main/p/python-biopython/python3-biopython_1.80+dfsg-4+b1_amd64.deb Size: 1593248 MD5sum: 87c665539ca8b339a1da0729e2afd5cf SHA256: 5888356eff82d5fd535ba4baff9f13dcadd7217fde56e9e1f805c253966923d8 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'show', '--no-all-versions', 'python3-biopython'] 0m59.7s INFO: apt-cache knows about the following packages: python3-biopython 0m59.7s INFO: Running scripts pre_install 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_database-server'] 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_database-server'] 0m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_exceptions'] 0m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_exceptions'] 0m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_extras'] 0m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_extras'] 0m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture'] 0m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture'] 0m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy'] 0m59.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy'] 0m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy', 'python3-biopython'] 0m59.9s DUMP: python3-biopython: Installed: 1.80+dfsg-4+b1 Candidate: 1.80+dfsg-4+b1 Version table: *** 1.80+dfsg-4+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy', 'python3-biopython'] 0m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-y', 'install', 'python3-biopython'] 1m0.2s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-biopython is already the newest version (1.80+dfsg-4+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-y', 'install', 'python3-biopython'] 1m0.2s INFO: Running scripts post_install 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_install_exceptions'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_install_exceptions'] 1m0.2s INFO: Running scripts post_distupgrade 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_exceptions'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_exceptions'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_zz_backports'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_distupgrade_zz_backports'] 1m0.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m1.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m1.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m1.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m1.9s INFO: Running scripts pre_install 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_database-server'] 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_database-server'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_exceptions'] 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_exceptions'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_extras'] 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_extras'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy'] 1m2.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy', 'python3-biopython'] 1m2.0s DUMP: python3-biopython: Installed: 1.80+dfsg-4+b1 Candidate: 1.80+dfsg-4+b1 Version table: *** 1.80+dfsg-4+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-cache', 'policy', 'python3-biopython'] 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-y', 'install', 'python3-biopython=1.80+dfsg-4+b1'] 1m2.3s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-biopython is already the newest version (1.80+dfsg-4+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', '-y', 'install', 'python3-biopython=1.80+dfsg-4+b1'] 1m2.3s INFO: Running scripts post_install 1m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_install_exceptions'] 1m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_install_exceptions'] 1m2.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m3.2s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 1m3.2s INFO: /bin converted to /usr/bin by /usr merge 1m3.2s INFO: /lib converted to /usr/lib by /usr merge 1m3.2s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m3.2s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m3.2s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m3.2s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m3.2s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m3.2s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 1m3.2s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 1m3.2s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 1m3.2s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 1m3.2s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 1m3.2s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 1m3.2s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 1m3.2s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 1m3.2s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 1m3.2s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 1m3.2s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 1m3.2s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 1m3.2s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 1m3.2s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 1m3.2s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 1m3.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m3.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m3.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m3.2s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m3.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m3.2s INFO: /sbin converted to /usr/sbin by /usr merge 1m4.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', '-ac', '--ignore-obsolete'] 1m5.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', '-ac', '--ignore-obsolete'] 1m5.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m5.4s DUMP: 0.15.6 1m5.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m5.4s INFO: Running adequate version 0.15.6 now. 1m5.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'python3-biopython'] 1m5.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'python3-biopython'] 1m5.5s INFO: Running scripts pre_remove 1m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_exceptions'] 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/pre_remove_exceptions'] 1m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m8.2s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 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 libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 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 libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libraqm0:amd64 libraqm0 0.7.0-4.1 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssl3:amd64 libssl3 3.0.13-1~deb12u2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.4-0.2+deb12u1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.4-0.2+deb12u1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 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 mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-biopython python3-biopython 1.80+dfsg-4+b1 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 install ok installed python3-pil:amd64 python3-pil 9.4.0-1.1+deb12u1 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-renderpm:amd64 python3-renderpm 3.6.12-1+b1 install ok installed python3-reportlab python3-reportlab 3.6.12-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.6.12-1+b1 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed readline-common readline-common 8.2-1.3 install ok installed sed sed 4.9-1 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'remove', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-biopython'] 1m45.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 72 to remove and 0 not upgraded. After this operation, 174 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12012 files and directories currently installed.) Removing python3-biopython (1.80+dfsg-4+b1) ... Removing python3-renderpm:amd64 (3.6.12-1+b1) ... Removing fonts-urw-base35 (20200910-7) ... Removing python3-numpy (1:1.24.2-1+deb12u1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-reportlab (3.6.12-1) ... Removing python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Removing libraqm0:amd64 (0.7.0-4.1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Removing python3-pkg-resources (66.1.1-1) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libfontenc1:amd64 (1:1.1.4-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.36.0-7+deb12u1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libopenjp2-7:amd64 (2.5.0-2) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libssl3:amd64 (3.0.13-1~deb12u2) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing media-types (10.0.0) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing readline-common (8.2-1.3) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.31) ... 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 libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libpng16-16:amd64 (1.6.39-2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 1m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'remove', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-biopython'] 1m45.3s INFO: Running scripts post_remove 1m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_remove_exceptions'] 1m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_remove_exceptions'] 1m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--purge', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m45.6s DUMP: (Reading database ... 6133 files and directories currently installed.) Purging configuration files for fonts-urw-base35 (20200910-7) ... dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 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 libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove 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 liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 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 libxau6 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 Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for perl (5.36.0-7+deb12u1) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for python3 (3.11.2-1+b1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.2-6+deb12u2) ... Purging configuration files for readline-common (8.2-1.3) ... Purging configuration files for sgml-base (1.31) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.18+nmu1) ... 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--purge', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--purge', 'python3-biopython'] 1m45.6s DUMP: dpkg: warning: ignoring request to remove python3-biopython which isn't installed 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--purge', 'python3-biopython'] 1m45.6s INFO: Running scripts post_purge 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_purge_exceptions'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_purge_exceptions'] 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--purge', '--pending'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--purge', '--pending'] 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--remove', '--pending'] 1m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg', '--remove', '--pending'] 1m45.6s INFO: Running scripts post_test 1m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_test_exceptions'] 1m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'tmp/scripts/post_test_exceptions'] 1m45.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m46.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg-divert', '--list'] 1m46.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'dpkg-divert', '--list'] 1m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'clean'] 1m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2', 'apt-get', 'clean'] 1m46.1s DEBUG: Recording chroot state 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/shm'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/shm'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/console'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/console'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/ptmx'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/ptmx'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/pts'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/dev/pts'] 1m47.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/proc'] 1m47.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2/proc'] 1m47.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m47.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpw3b9j1j2'] 1m47.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpw3b9j1j2 1m47.2s INFO: PASS: Upgrading between Debian distributions. 1m47.2s INFO: PASS: All tests. 1m47.2s INFO: piuparts run ends. ret=0 End: 2024-08-21 06:23:30 GMT