Start: 2025-02-01 22:38:17 GMT [testing] Package: hinge Source: hinge (0.5.0-7) Version: 0.5.0-7+b2 Installed-Size: 3076 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libfmt10 (>= 10.1.1+ds1), libgcc-s1 (>= 3.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib Description: long read genome assembler based on hinging Homepage: https://github.com/HingeAssembler/HINGE Description-md5: 796f6bb30e0dd11acb73bb5eeeaf4c08 Section: science Priority: optional Filename: pool/main/h/hinge/hinge_0.5.0-7+b2_amd64.deb Size: 474188 MD5sum: 9215baedfa3408e8a5b12fedf32bc1e6 SHA256: 2e40dd416b4271acf162211f96904a228d54a53c615e7e815eb2f8547a0205fc [sid] Package: hinge Source: hinge (0.5.0-7) Version: 0.5.0-7+b3 Installed-Size: 3096 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libfmt10 (>= 10.1.1+ds1), libgcc-s1 (>= 3.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib Description: long read genome assembler based on hinging Homepage: https://github.com/HingeAssembler/HINGE Description-md5: 796f6bb30e0dd11acb73bb5eeeaf4c08 Section: science Priority: optional Filename: pool/main/h/hinge/hinge_0.5.0-7+b3_amd64.deb Size: 477416 MD5sum: 6cb86b393d16f7bd532afd92345c2246 SHA256: 1c5d68715adc3b49c32dbadbd23a1899b2bbac8d712abf8f4a66d4ad8d7c8c68 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt hinge=0.5.0-7+b3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt hinge=0.5.0-7+b3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpaptdttgi 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpaptdttgi 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpaptdttgi/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9419 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6319 kB] Fetched 15.9 MB in 1s (20.2 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: liblz4-1 libselinux1 libsemanage-common libsemanage2 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 239 kB of archives. After this operation, 3072 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.10.0-3 [63.8 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.7-3.1 [76.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.7-2.1 [7208 B] Get:4 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.7-2.1 [91.2 kB] Fetched 239 kB in 0s (15.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5029 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.10.0-3_amd64.deb ... Unpacking liblz4-1:amd64 (1.10.0-3) over (1.9.4-4) ... Setting up liblz4-1:amd64 (1.10.0-3) ... (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 ... 5029 files and directories currently installed.) Preparing to unpack .../libselinux1_3.7-3.1_amd64.deb ... Unpacking libselinux1:amd64 (3.7-3.1) over (3.7-3+b1) ... Setting up libselinux1:amd64 (3.7-3.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5028 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.7-2.1_all.deb ... Unpacking libsemanage-common (3.7-2.1) over (3.7-2) ... Preparing to unpack .../libsemanage2_3.7-2.1_amd64.deb ... Unpacking libsemanage2:amd64 (3.7-2.1) over (3.7-2+b1) ... Setting up libsemanage-common (3.7-2.1) ... Setting up libsemanage2:amd64 (3.7-2.1) ... Processing triggers for libc-bin (2.40-6) ... 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s DUMP: 972032b9c41ddeceff1b4ab45f12c0a7 - 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s INFO: Running scripts post_setup 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_dummy_users'] 0m2.6s 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 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_dummy_users'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_forbid_home'] 0m2.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_forbid_home'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.6s 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' 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_minimize'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_minimize'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_zz_backports'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_setup_zz_backports'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.6s DUMP: install ok installed apt apt 2.9.23 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.4-1 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-11 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-12 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.23 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblkid1:amd64 libblkid1 2.40.4-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-6 install ok installed libc6:amd64 libc6 2.40-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-12 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.4-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3.1 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-1 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-12 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libuuid1:amd64 libuuid1 2.40.4-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-1 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.4-1 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2024b-6 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m2.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m2.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m2.8s INFO: Running scripts is_testable 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/is_testable_uninstallable'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/is_testable_uninstallable'] 0m2.8s INFO: Running scripts pre_test 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_test_exceptions'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_test_exceptions'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_test_root_password'] 0m2.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_test_root_password'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'show', '--no-all-versions', 'hinge'] 0m3.0s DUMP: Package: hinge Source: hinge (0.5.0-7) Version: 0.5.0-7+b2 Installed-Size: 3076 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libfmt10 (>= 10.1.1+ds1), libgcc-s1 (>= 3.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib Description-en: long read genome assembler based on hinging HINGE is a genome assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding ??hinges?? to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers. Description-md5: 796f6bb30e0dd11acb73bb5eeeaf4c08 Homepage: https://github.com/HingeAssembler/HINGE Section: science Priority: optional Filename: pool/main/h/hinge/hinge_0.5.0-7+b2_amd64.deb Size: 474188 MD5sum: 9215baedfa3408e8a5b12fedf32bc1e6 SHA256: 2e40dd416b4271acf162211f96904a228d54a53c615e7e815eb2f8547a0205fc 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'show', '--no-all-versions', 'hinge'] 0m3.0s INFO: apt-cache knows about the following packages: hinge 0m3.0s INFO: Running scripts pre_install 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_database-server'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_database-server'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_exceptions'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_exceptions'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_extras'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_extras'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy'] 0m3.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy', 'hinge'] 0m3.1s DUMP: hinge: Installed: (none) Candidate: 0.5.0-7+b2 Version table: 0.5.0-7+b2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy', 'hinge'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-y', 'install', 'hinge'] 0m40.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt daligner dascrubber dazzdb fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libdeflate0 libdouble-conversion3 libexpat1 libffi8 libfmt10 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libicu72 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtasn1-6 libtcl8.6 libtiff6 libtk8.6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-chardet python3-colormap python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-packaging python3-pbcore python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-ujson python3-unicodedata2 python3.12-tk python3.13 python3.13-minimal python3.13-tk readline-common sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre rng-tools low-memory-monitor gnutls-bin krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pbcore-doc python-pil-doc python3-setuptools python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python-biopython-doc ncbi-blast+ python3-bs4 python3-cssselect python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-yaml python3-h5py python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-pooch isympy-common The following NEW packages will be installed: blt daligner dascrubber dazzdb fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 hinge libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libdeflate0 libdouble-conversion3 libexpat1 libffi8 libfmt10 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libicu72 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtasn1-6 libtcl8.6 libtiff6 libtk8.6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-chardet python3-colormap python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-packaging python3-pbcore python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-ujson python3-unicodedata2 python3.12-tk python3.13 python3.13-minimal python3.13-tk readline-common sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 130 MB of archives. After this operation, 589 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:28 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:42 http://deb.debian.org/debian trixie/main amd64 daligner amd64 1.0+git20240119.335105d-3 [242 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 dascrubber amd64 1.1-4 [168 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 dazzdb amd64 1.0+git20240115.be65e59-1 [227 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-12 [137 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libdouble-conversion3 amd64 3.3.0-1+b3 [41.9 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 python3-ujson amd64 5.10.0-1+b3 [25.5 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-12 [9300 B] Get:64 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1.1 [522 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.8-5 [113 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.1-3 [103 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.13.1-1 [9464 B] Get:80 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1.1 [79.6 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:84 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-6 [95.1 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-3+b1 [20.5 MB] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 python3-attr all 24.3.0-1 [68.8 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.55.3-2 [1633 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b3 [5650 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-colormap all 1.3.0-1 [17.6 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.84+dfsg-4+b2 [1651 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:130 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 python3-pbcore all 2.1.2+dfsg-10 [2831 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:153 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:156 http://deb.debian.org/debian trixie/main amd64 hinge amd64 0.5.0-7+b2 [474 kB] Preconfiguring packages ... Fetched 130 MB in 1s (103 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5031 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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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 (8.2-6) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../08-libpython3.13-stdlib_3.13.1-3_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.1-3) ... 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Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-12) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up unicode-data (15.1.0-1) ... Setting up dazzdb (1.0+git20240115.be65e59-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... 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No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.1-3) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up python3.12-tk (3.12.8-5) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-freetype (2.5.1-1) ... 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Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-fonttools (4.55.3-2) ... Setting up python3-matplotlib (3.8.3-3+b3) ... Setting up python3-colormap (1.3.0-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b2) ... Setting up python3-pbcore (2.1.2+dfsg-10) ... Setting up hinge (0.5.0-7+b2) ... 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-y', 'install', 'hinge'] 0m40.2s INFO: Running scripts post_install 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_install_exceptions'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_install_exceptions'] 0m40.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m40.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m40.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpaptdttgi to sid 0m40.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m40.9s INFO: Running scripts pre_distupgrade 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_exceptions'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_exceptions'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'update'] 0m42.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7343 kB] Fetched 17.6 MB in 2s (11.5 MB/s) Reading package lists... 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'update'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-yf', 'dist-upgrade'] 0m50.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: python3-numpy-dev The following packages will be upgraded: apt bsdutils dpkg gcc-14-base hinge libapt-pkg6.0t64 libatomic1 libblas3 libblkid1 libgcc-s1 libgfortran5 libgomp1 liblapack3 libmount1 libncursesw6 libopenjp2-7 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16t64 libsmartcols1 libstdc++6 libtinfo6 libuuid1 libxxhash0 login mount ncurses-base ncurses-bin python3-biopython python3-kiwisolver python3-numpy python3-pil python3-pil.imagetk python3-scipy tzdata util-linux 38 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 44.2 MB of archives. After this operation, 8119 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-2 [106 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-16 [9296 B] Get:3 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-16 [137 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get:5 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-16 [48.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-16 [72.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-16 [713 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.26 [1115 kB] Get:10 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.14 [1537 kB] Get:11 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20250125-2 [438 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-2 [36.3 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.4-2 [169 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.4-2 [199 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-2 [140 kB] Get:16 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-2 [1213 kB] Get:17 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-2 [155 kB] Get:18 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.26 [1433 kB] Get:19 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20250125-2 [273 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.7.0-2 [69.8 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.7.0-2 [48.8 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.7.0-2 [177 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.7.0-2 [248 kB] Get:24 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-2 [88.4 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20250125-2 [348 kB] Get:27 http://deb.debian.org/debian sid/main amd64 tzdata all 2025a-1 [259 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:29 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:30 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.14.1-4 [20.5 MB] Get:31 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.85+dfsg-1 [1674 kB] Get:32 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.2+ds-2 [7507 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.2+ds-2 [138 kB] Get:34 http://deb.debian.org/debian sid/main amd64 hinge amd64 0.5.0-7+b3 [477 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get:37 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.7-3 [76.9 kB] Get:38 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 11.1.0-4 [81.4 kB] Get:39 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 11.1.0-4 [528 kB] Preconfiguring packages ... Fetched 44.2 MB in 0s (111 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19935 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.4-2_amd64.deb ... Unpacking bsdutils (1:2.40.4-2) over (1:2.40.4-1) ... Setting up bsdutils (1:2.40.4-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19932 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.4-2_amd64.deb ... Unpacking util-linux (2.40.4-2) over (2.40.4-1) ... Setting up util-linux (2.40.4-2) ... (Reading database ... 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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 ... 19932 files and directories currently installed.) Preparing to unpack .../libpam0g_1.7.0-2_amd64.deb ... Unpacking libpam0g:amd64 (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam0g:amd64 (1.7.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19931 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.7.0-2_amd64.deb ... Unpacking libpam-modules-bin (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam-modules-bin (1.7.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19922 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.7.0-2_amd64.deb ... Unpacking libpam-modules:amd64 (1.7.0-2) over (1.5.3-7+b1) ... Setting up libpam-modules:amd64 (1.7.0-2) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/namespace.init ... Installing new version of config file /etc/security/pwhistory.conf ... (Reading database ... (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 ... 19870 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.7.0-2_all.deb ... Unpacking libpam-runtime (1.7.0-2) over (1.5.3-7) ... Setting up libpam-runtime (1.7.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19931 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.40.4-2_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.4-2) over (1:4.16.0-2+really2.40.4-1) ... Preparing to unpack .../libncursesw6_6.5+20250125-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250125-2) over (6.5-2+b1) ... Preparing to unpack .../libtinfo6_6.5+20250125-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.5+20250125-2) over (6.5-2+b1) ... Setting up libtinfo6:amd64 (6.5+20250125-2) ... (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 ... 19930 files and directories currently installed.) Preparing to unpack .../00-tzdata_2025a-1_all.deb ... Unpacking tzdata (2025a-1) over (2024b-6) ... Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) over (3.12.0-4) ... Preparing to unpack .../02-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) over (3.12.0-4) ... Preparing to unpack .../03-python3-scipy_1.14.1-4_amd64.deb ... Unpacking python3-scipy (1.14.1-4) over (1.14.1-3+b1) ... Preparing to unpack .../04-python3-biopython_1.85+dfsg-1_amd64.deb ... Unpacking python3-biopython (1.85+dfsg-1) over (1.84+dfsg-4+b2) ... Preparing to unpack .../05-python3-numpy_1%3a2.2.2+ds-2_amd64.deb ... Unpacking python3-numpy (1:2.2.2+ds-2) over (1:1.26.4+ds-13) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../06-python3-numpy-dev_1%3a2.2.2+ds-2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Preparing to unpack .../07-hinge_0.5.0-7+b3_amd64.deb ... Unpacking hinge (0.5.0-7+b3) over (0.5.0-7+b2) ... Preparing to unpack .../08-libopenjp2-7_2.5.3-1_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.3-1) over (2.5.0-2+b4) ... Preparing to unpack .../09-libpng16-16t64_1.6.46-4_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.46-4) over (1.6.44-3) ... Preparing to unpack .../10-python3-kiwisolver_1.4.7-3_amd64.deb ... Unpacking python3-kiwisolver (1.4.7-3) over (1.4.7-2+b1) ... Preparing to unpack .../11-python3-pil.imagetk_11.1.0-4_amd64.deb ... Unpacking python3-pil.imagetk:amd64 (11.1.0-4) over (10.4.0-1.1) ... Preparing to unpack .../12-python3-pil_11.1.0-4_amd64.deb ... Unpacking python3-pil:amd64 (11.1.0-4) over (10.4.0-1.1) ... Setting up libgomp1:amd64 (14.2.0-16) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 1 22:39:04 UTC 2025. Universal Time is now: Sat Feb 1 22:39:04 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libblas3:amd64 (3.12.1-2) ... Setting up python3-kiwisolver (1.4.7-3) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Setting up libatomic1:amd64 (14.2.0-16) ... Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up mount (2.40.4-2) ... Setting up libopenjp2-7:amd64 (2.5.3-1) ... Setting up login (1:4.16.0-2+really2.40.4-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... Setting up python3-pil:amd64 (11.1.0-4) ... Setting up python3-pil.imagetk:amd64 (11.1.0-4) ... Setting up python3-numpy (1:2.2.2+ds-2) ... Setting up python3-biopython (1.85+dfsg-1) ... Setting up python3-scipy (1.14.1-4) ... Setting up hinge (0.5.0-7+b3) ... Processing triggers for libc-bin (2.40-6) ... 0m50.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-yf', 'dist-upgrade'] 0m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m51.3s DUMP: 2c0679303be027c3aad520c3fd7d5131 - 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m51.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'show', '--no-all-versions', 'hinge'] 0m51.4s DUMP: Package: hinge Source: hinge (0.5.0-7) Version: 0.5.0-7+b3 Installed-Size: 3096 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libfmt10 (>= 10.1.1+ds1), libgcc-s1 (>= 3.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib Description-en: long read genome assembler based on hinging HINGE is a genome assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding ??hinges?? to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers. Description-md5: 796f6bb30e0dd11acb73bb5eeeaf4c08 Homepage: https://github.com/HingeAssembler/HINGE Section: science Priority: optional Filename: pool/main/h/hinge/hinge_0.5.0-7+b3_amd64.deb Size: 477416 MD5sum: 6cb86b393d16f7bd532afd92345c2246 SHA256: 1c5d68715adc3b49c32dbadbd23a1899b2bbac8d712abf8f4a66d4ad8d7c8c68 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'show', '--no-all-versions', 'hinge'] 0m51.4s INFO: apt-cache knows about the following packages: hinge 0m51.4s INFO: Running scripts pre_install 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_database-server'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_database-server'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_exceptions'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_exceptions'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_extras'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_extras'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy'] 0m51.5s 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: 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy', 'hinge'] 0m51.5s DUMP: hinge: Installed: 0.5.0-7+b3 Candidate: 0.5.0-7+b3 Version table: *** 0.5.0-7+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy', 'hinge'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-y', 'install', 'hinge'] 0m51.8s DUMP: Reading package lists... Building dependency tree... Reading state information... hinge is already the newest version (0.5.0-7+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-y', 'install', 'hinge'] 0m51.8s INFO: Running scripts post_install 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_install_exceptions'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_install_exceptions'] 0m51.8s INFO: Running scripts post_distupgrade 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_exceptions'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_exceptions'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_zz_backports'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_distupgrade_zz_backports'] 0m51.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m52.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m52.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m53.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m53.2s INFO: Running scripts pre_install 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_database-server'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_database-server'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_exceptions'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_exceptions'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_extras'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_extras'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy'] 0m53.3s 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: 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy', 'hinge'] 0m53.3s DUMP: hinge: Installed: 0.5.0-7+b3 Candidate: 0.5.0-7+b3 Version table: *** 0.5.0-7+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-cache', 'policy', 'hinge'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-y', 'install', 'hinge=0.5.0-7+b3'] 0m53.6s DUMP: Reading package lists... Building dependency tree... Reading state information... hinge is already the newest version (0.5.0-7+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', '-y', 'install', 'hinge=0.5.0-7+b3'] 0m53.6s INFO: Running scripts post_install 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_install_exceptions'] 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_install_exceptions'] 0m53.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m54.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 0m55.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', '-ac', '--ignore-obsolete'] 0m56.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', '-ac', '--ignore-obsolete'] 0m56.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m56.7s DUMP: 0.15.6 0m56.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m56.7s INFO: Running adequate version 0.15.6 now. 0m56.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'hinge'] 0m56.7s DUMP: hinge: py-file-not-bytecompiled /usr/lib/hinge/add_groundtruth_json.py hinge: py-file-not-bytecompiled /usr/lib/hinge/clip_ends.py hinge: py-file-not-bytecompiled /usr/lib/hinge/compute_n50_from_draft.py hinge: py-file-not-bytecompiled /usr/lib/hinge/create_hgraph_nogt.py hinge: py-file-not-bytecompiled /usr/lib/hinge/download_NCTC_pipeline.py hinge: py-file-not-bytecompiled /usr/lib/hinge/get_NCTC_json.py hinge: py-file-not-bytecompiled /usr/lib/hinge/get_single_strand.py 0m56.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'hinge'] 0m56.7s ERROR: WARN: Inadequate results from running adequate! hinge: py-file-not-bytecompiled /usr/lib/hinge/add_groundtruth_json.py hinge: py-file-not-bytecompiled /usr/lib/hinge/clip_ends.py hinge: py-file-not-bytecompiled /usr/lib/hinge/compute_n50_from_draft.py hinge: py-file-not-bytecompiled /usr/lib/hinge/create_hgraph_nogt.py hinge: py-file-not-bytecompiled /usr/lib/hinge/download_NCTC_pipeline.py hinge: py-file-not-bytecompiled /usr/lib/hinge/get_NCTC_json.py hinge: py-file-not-bytecompiled /usr/lib/hinge/get_single_strand.py 0m56.7s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 0m56.7s INFO: Running scripts pre_remove 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m58.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m58.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_exceptions'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/pre_remove_exceptions'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m58.2s DUMP: install ok installed apt apt 2.9.26 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.4-2 install ok installed coreutils coreutils 9.5-1+b1 install ok installed daligner daligner 1.0+git20240119.335105d-3 install ok installed dascrubber dascrubber 1.1-4 install ok installed dash dash 0.5.12-11 install ok installed dazzdb dazzdb 1.0+git20240115.be65e59-1 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.14 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.3-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-16 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hinge hinge 0.5.0-7+b3 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.26 install ok installed libatomic1:amd64 libatomic1 14.2.0-16 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.40.4-2 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-6 install ok installed libc6:amd64 libc6 2.40-6 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.11.1-1+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libdouble-conversion3:amd64 libdouble-conversion3 3.3.0-1+b3 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfmt10:amd64 libfmt10 10.1.1+ds1-4 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-16 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.4-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-16 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-4 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libicu72:amd64 libicu72 72.1-6 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-4 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-4 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.4-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250125-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.6.0-2 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.9.1-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.9.1-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-2 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-2 install ok installed libpam-runtime libpam-runtime 1.7.0-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.46-4 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.1-2 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.1-3 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.1-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3.1 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250125-2 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-2 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b4 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-2 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.4-2 install ok installed ncurses-base ncurses-base 6.5+20250125-2 install ok installed ncurses-bin ncurses-bin 6.5+20250125-2 install ok installed netbase netbase 6.4 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.13.1-2 install ok installed python3-attr python3-attr 24.3.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.85+dfsg-1 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 install ok installed python3-cairo python3-cairo 1.26.1-2+b1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-colormap python3-colormap 1.3.0-1 install ok installed python3-contourpy python3-contourpy 1.3.1-1 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-fonttools python3-fonttools 4.55.3-2 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-6 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1+b1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-1 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3+b3 install ok installed python3-minimal python3-minimal 3.13.1-2 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-networkx python3-networkx 3.2.1-5 install ok installed python3-numpy python3-numpy 1:2.2.2+ds-2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.2+ds-2 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pbcore python3-pbcore 2.1.2+dfsg-10 install ok installed python3-pil:amd64 python3-pil 11.1.0-4 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-4 install ok installed python3-pkg-resources python3-pkg-resources 75.6.0-1 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b2 install ok installed python3-reportlab python3-reportlab 4.2.5-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.14.1-4 install ok installed python3-sympy python3-sympy 1.13.3-1 install ok installed python3-tk:amd64 python3-tk 3.13.1-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2024.2-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.0+dfsg1-1 install ok installed python3-ujson:amd64 python3-ujson 5.10.0-1+b3 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3.12-tk python3.12-tk 3.12.8-5 install ok installed python3.13 python3.13 3.13.1-3 install ok installed python3.13-minimal python3.13-minimal 3.13.1-3 install ok installed python3.13-tk python3.13-tk 3.13.1-3 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2025a-1 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-2 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'remove', 'blt', 'daligner', 'dascrubber', 'dazzdb', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfmt10:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-colormap', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pbcore', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-ujson:amd64', 'python3-unicodedata2', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'hinge'] 1m18.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt daligner dascrubber dazzdb fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 hinge libatomic1 libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libdeflate0 libdouble-conversion3 libexpat1 libffi8 libfmt10 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libicu72 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtasn1-6 libtcl8.6 libtiff6 libtk8.6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-cairo python3-chardet python3-colormap python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-networkx python3-numpy python3-numpy-dev python3-packaging python3-pbcore python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-ujson python3-unicodedata2 python3.12-tk python3.13 python3.13-minimal python3.13-tk readline-common sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 157 to remove and 0 not upgraded. After this operation, 597 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 ... 19984 files and directories currently installed.) Removing hinge (0.5.0-7+b3) ... Removing python3-pbcore (2.1.2+dfsg-10) ... Removing python3-biopython (1.85+dfsg-1) ... Removing python3-reportlab (4.2.5-1) ... Removing python3-colormap (1.3.0-1) ... Removing python3-matplotlib (3.8.3-3+b3) ... Removing python3-pil.imagetk:amd64 (11.1.0-4) ... Removing python3-pil:amd64 (11.1.0-4) ... Removing python3-tk:amd64 (3.13.1-1) ... Removing blt (2.5.3+dfsg-7) ... Removing daligner (1.0+git20240119.335105d-3) ... Removing dascrubber (1.1-4) ... Removing dazzdb (1.0+git20240115.be65e59-1) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.1-3) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2+b1) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.3-1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1) ... Removing libglib2.0-0t64:amd64 (2.82.4-2) ... Removing libatomic1:amd64 (14.2.0-16) ... Removing python3-contourpy (1.3.1-1) ... Removing python3-freetype (2.5.1-1) ... Removing python3-pysam (0.22.1+ds-2+b2) ... Removing libhts3t64:amd64 (1.20+ds-2) ... Removing libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.23-1+b1) ... Removing python3-ujson:amd64 (5.10.0-1+b3) ... Removing libdouble-conversion3:amd64 (3.3.0-1+b3) ... Removing python3-networkx (3.2.1-5) ... Removing python3-pkg-resources (75.6.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libfmt10:amd64 (10.1.1+ds1-4) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-16) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libgssapi-krb5-2:amd64 (1.21.3-4) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libkrb5-3:amd64 (1.21.3-4) ... Removing libk5crypto3:amd64 (1.21.3-4) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-4) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.9+dfsg-1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.6.0-2) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Removing libngtcp2-16:amd64 (1.9.1-1) ... Removing libopenjp2-7:amd64 (2.5.3-1) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Removing libwebpmux3:amd64 (1.5.0-0.1) ... Removing libwebpdemux2:amd64 (1.5.0-0.1) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing python3.12-tk (3.12.8-5) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-kiwisolver (1.4.7-3) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-packaging (24.2-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing libfontconfig1:amd64 (2.15.0-2) ... Removing fontconfig-config (2.15.0-2) ... Removing fonts-urw-base35 (20200910-8) ... Removing xfonts-utils (1:7.7+7) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libgnutls30t64:amd64 (3.8.8-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libidn2-0:amd64 (2.3.7-2+b1) ... Removing libpng16-16t64:amd64 (1.6.46-4) ... Removing libtasn1-6:amd64 (4.19.0-3+b3) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libunistring5:amd64 (1.3-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b4) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing python3-ufolib2 (0.17.0+dfsg1-1) ... Removing python3-attr (24.3.0-1) ... Removing python3-fonttools (4.55.3-2) ... Removing python3-scipy (1.14.1-4) ... Removing python3-numpy (1:2.2.2+ds-2) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-sympy (1.13.3-1) ... Removing python3-lz4 (4.4.0+dfsg-1) ... Removing python3-fs (2.4.16-6) ... Removing python3-tz (2024.2-1) ... Removing python3-lxml:amd64 (5.3.0-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing libgcrypt20:amd64 (1.11.0-7) ... Removing libgfortran5:amd64 (14.2.0-16) ... Removing libgpg-error0:amd64 (1.51-3) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-6) ... Removing python3-brotli (1.1.0-2+b6) ... Removing python3-decorator (5.1.1-5) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Removing python3-platformdirs (4.3.6-1) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.13.1-2) ... Removing python3.13 (3.13.1-3) ... Removing python3-minimal (3.13.1-2) ... Removing python3.13-minimal (3.13.1-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.13.1-2) ... Removing libpython3.13-stdlib:amd64 (3.13.1-3) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.6-1) ... Removing libncursesw6:amd64 (6.5+20250125-2) ... Removing libpython3.13-minimal:amd64 (3.13.1-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-6) ... 1m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'remove', 'blt', 'daligner', 'dascrubber', 'dazzdb', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfmt10:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-colormap', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pbcore', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-ujson:amd64', 'python3-unicodedata2', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'hinge'] 1m18.5s INFO: Running scripts post_remove 1m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_remove_exceptions'] 1m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_remove_exceptions'] 1m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--purge', 'blt', 'daligner', 'dascrubber', 'dazzdb', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfmt10:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-colormap', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pbcore', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-ujson:amd64', 'python3-unicodedata2', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m18.7s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed dpkg: warning: ignoring request to remove daligner which isn't installed dpkg: warning: ignoring request to remove dascrubber which isn't installed dpkg: warning: ignoring request to remove dazzdb which isn't installed (Reading database ... 5084 files and directories currently installed.) Purging configuration files for fontconfig-config (2.15.0-2) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdouble-conversion3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libfmt10 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcrypt20 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.4-2) ... dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpg-error0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-4) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove 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 libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.1-3) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.13.1-2) ... dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-colormap which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pbcore which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed Purging configuration files for python3-sympy (1.13.3-1) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-ujson which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3.12-tk which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.1-3) ... dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for readline-common (8.2-6) ... Purging configuration files for sgml-base (1.31) ... dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+24) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 1m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--purge', 'blt', 'daligner', 'dascrubber', 'dazzdb', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfmt10:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-chardet', 'python3-colormap', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pbcore', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-ujson:amd64', 'python3-unicodedata2', 'python3.12-tk', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--purge', 'hinge'] 1m18.7s DUMP: dpkg: warning: ignoring request to remove hinge which isn't installed 1m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--purge', 'hinge'] 1m18.7s INFO: Running scripts post_purge 1m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_purge_exceptions'] 1m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_purge_exceptions'] 1m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--purge', '--pending'] 1m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--purge', '--pending'] 1m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--remove', '--pending'] 1m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg', '--remove', '--pending'] 1m18.7s INFO: Running scripts post_test 1m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_test_exceptions'] 1m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'tmp/scripts/post_test_exceptions'] 1m18.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 1m18.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg-divert', '--list'] 1m18.9s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'dpkg-divert', '--list'] 1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'clean'] 1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpaptdttgi', 'apt-get', 'clean'] 1m18.9s DEBUG: Recording chroot state 1m19.2s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 1m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/shm'] 1m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/shm'] 1m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/console'] 1m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/console'] 1m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/ptmx'] 1m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/ptmx'] 1m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/pts'] 1m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/dev/pts'] 1m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/proc'] 1m19.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpaptdttgi/proc'] 1m19.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 1m19.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpaptdttgi'] 1m19.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpaptdttgi 1m19.6s INFO: PASS: Upgrading between Debian distributions. 1m19.6s INFO: PASS: All tests. 1m19.6s INFO: piuparts run ends. ret=0 End: 2025-02-01 22:39:37 GMT