Start: 2025-02-10 03:39:21 GMT Package: snakemake Version: 7.32.4-7 Installed-Size: 1560 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-configargparse, python3-connection-pool, python3-datrie, python3-docutils, python3-git, python3-humanfriendly, python3-jinja2 (>= 3.0~), python3-jsonschema, python3-nbformat, python3-packaging, python3-platformdirs, python3-psutil, python3-pulp (>= 2.0~), python3-requests, python3-retry, python3-smart-open (>= 3.0~), python3-stopit, python3-tabulate, python3-throttler, python3-toposort, python3-wrapt, python3-yaml, python3-yte, python3:any, ca-certificates, python3-ratelimiter, libjs-bootstrap, libjs-jquery Recommends: cwltool, imagemagick, python3-tz, python3-yappi, python3-pygments, python3-azure-storage, python3-biopython, python3-boto3, python3-botocore, python3-dropbox, python3-flask, python3-ftputil, python3-irodsclient, python3-kubernetes, python3-urllib3 Suggests: slurm-client, snakemake-doc Description: pythonic workflow management system Homepage: https://snakemake.readthedocs.io/ Description-md5: 7f9c57469c639aa1e67301b2a7ed865e Section: science Priority: optional Filename: pool/main/s/snakemake/snakemake_7.32.4-7_all.deb Size: 317768 MD5sum: eb123fb77f41a14df62a9f6674816ee6 SHA256: 423dc96d06568c8384763a0d39b21a3d1329b3dd4c1a60d8c1a713b32f48801a 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt snakemake=7.32.4-7 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt snakemake=7.32.4-7 0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmp7_ah5bgi 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp7_ah5bgi 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmp7_ah5bgi/tmp/scripts/ 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp7_ah5bgi/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'update'] 0m2.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7351 kB] Fetched 17.6 MB in 2s (9477 kB/s) Reading package lists... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'update'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', '-yf', 'dist-upgrade'] 0m4.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2559 kB of archives. After this operation, 4096 B disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.28 [1119 kB] Get:2 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.28 [1440 kB] Fetched 2559 kB in 0s (42.4 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 ... 5022 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.28_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.28) over (2.9.27) ... Setting up libapt-pkg6.0t64:amd64 (2.9.28) ... (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 ... 5022 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.28_amd64.deb ... Unpacking apt (2.9.28) over (2.9.27) ... Setting up apt (2.9.28) ... Processing triggers for libc-bin (2.40-6) ... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', '-yf', 'dist-upgrade'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s DUMP: c61adbb621f2dada46ffe3b1ee31e397 - 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s INFO: Running scripts post_setup 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_dummy_users'] 0m6.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_dummy_users'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_forbid_home'] 0m6.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_forbid_home'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_minimize'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_minimize'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_zz_backports'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_setup_zz_backports'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'clean'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'clean'] 0m6.9s DEBUG: Recording chroot state 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.5s DUMP: install ok installed apt apt 2.9.28 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 1:2.40.4-3 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 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 1.22.15 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 14.2.0-16 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 2.9.28 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 2.40.4-3 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 14.2.0-16 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 2.40.4-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 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 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.8-1 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 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-3 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 14.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 257.2-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250125-2 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libuuid1:amd64 libuuid1 2.40.4-3 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+really2.40.4-3 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 1.3.4.20250131-1 install ok installed mount mount 2.40.4-3 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 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 1.2.1-6 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 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-divert', '--list'] 0m7.5s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-divert', '--list'] 0m7.5s INFO: Running scripts is_testable 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/is_testable_uninstallable'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/is_testable_uninstallable'] 0m7.5s INFO: apt-cache does not know about any of the requested packages 0m7.5s INFO: Running scripts pre_test 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_test_exceptions'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_test_exceptions'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_test_root_password'] 0m7.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_test_root_password'] 0m7.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m8.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m8.8s DEBUG: No broken symlinks as far as we can find. 0m8.8s INFO: Running scripts pre_install 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_database-server'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_database-server'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_exceptions'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_exceptions'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_extras'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_extras'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_log_alternatives'] 0m8.8s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_install_log_alternatives'] 0m8.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m9.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m9.7s DEBUG: No broken symlinks as far as we can find. 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-cache', 'policy'] 0m10.6s 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: 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-cache', 'policy'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-cache', 'policy', 'snakemake'] 0m10.7s DUMP: snakemake: Installed: (none) Candidate: 7.32.4-7 Version table: 7.32.4-7 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-cache', 'policy', 'snakemake'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', '-y', 'install', 'snakemake=7.32.4-7'] 0m31.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common fonts-glyphicons-halflings git git-man libblas3 libbrotli1 libcurl3t64-gnutls libdatrie1 liberror-perl libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgnutls30t64 libgssapi-krb5-2 libidn2-0 libjs-bootstrap libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libperl5.40 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtasn1-6 libunistring5 libyaml-0-2 media-types netbase openssl perl perl-modules-5.40 python3 python3-attr python3-autocommand python3-certifi python3-chardet python3-charset-normalizer python3-configargparse python3-connection-pool python3-datrie python3-decorator python3-docutils python3-dpath python3-fastjsonschema python3-git python3-gitdb python3-humanfriendly python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-markupsafe python3-minimal python3-more-itertools python3-nbformat python3-packaging python3-pkg-resources python3-plac python3-platformdirs python3-psutil python3-pulp python3-py python3-pyparsing python3-ratelimiter python3-referencing python3-requests python3-retry python3-roman python3-rpds-py python3-smart-open python3-smmap python3-stopit python3-tabulate python3-throttler python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-urllib3 python3-wrapt python3-yaml python3-yte python3.13 python3.13-minimal readline-common sgml-base xml-core Suggested packages: gettext-base git-doc git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn gdbm-l10n gnutls-bin krb5-doc krb5-user sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python-attr-doc python-charset-normalizer-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-fastjsonschema-doc python-git-doc python-jinja2-doc python-jsonschema-doc python-jupyter-core-doc python3-pip python3-setuptools subversion python3-pytest python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python3-azure python3-azure-storage python-traitlets-doc python3-brotli python3.13-venv python3.13-doc binutils binfmt-support readline-doc sgml-base-doc slurm-client snakemake-doc debhelper Recommended packages: patch less ssh-client javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libpaper-utils python3-pil python3-pygments python3-babel python3-fqdn python3-isoduration python3-json-pointer python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-uritemplate python3-webcolors python3-boto3 python3-paramiko python3-zstandard cwltool imagemagick python3-tz python3-yappi python3-azure-storage python3-biopython python3-botocore python3-dropbox python3-flask python3-ftputil python3-irodsclient python3-kubernetes The following NEW packages will be installed: ca-certificates coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common fonts-glyphicons-halflings git git-man libblas3 libbrotli1 libcurl3t64-gnutls libdatrie1 liberror-perl libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgnutls30t64 libgssapi-krb5-2 libidn2-0 libjs-bootstrap libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libperl5.40 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtasn1-6 libunistring5 libyaml-0-2 media-types netbase openssl perl perl-modules-5.40 python3 python3-attr python3-autocommand python3-certifi python3-chardet python3-charset-normalizer python3-configargparse python3-connection-pool python3-datrie python3-decorator python3-docutils python3-dpath python3-fastjsonschema python3-git python3-gitdb python3-humanfriendly python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-markupsafe python3-minimal python3-more-itertools python3-nbformat python3-packaging python3-pkg-resources python3-plac python3-platformdirs python3-psutil python3-pulp python3-py python3-pyparsing python3-ratelimiter python3-referencing python3-requests python3-retry python3-roman python3-rpds-py python3-smart-open python3-smmap python3-stopit python3-tabulate python3-throttler python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-urllib3 python3-wrapt python3-yaml python3-yte python3.13 python3.13-minimal readline-common sgml-base snakemake xml-core 0 upgraded, 118 newly installed, 0 to remove and 0 not upgraded. Need to get 43.6 MB of archives. After this operation, 190 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:5 http://deb.debian.org/debian sid/main amd64 media-types all 11.0.0 [27.6 kB] Get:6 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get:13 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:16 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:17 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:18 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20241223 [164 kB] Get:19 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:23 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-8 [267 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get:26 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:27 http://deb.debian.org/debian sid/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-3 [458 kB] Get:28 http://deb.debian.org/debian sid/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-1+b1 [293 kB] Get:29 http://deb.debian.org/debian sid/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get:30 http://deb.debian.org/debian sid/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get:31 http://deb.debian.org/debian sid/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get:32 http://deb.debian.org/debian sid/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get:33 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:34 http://deb.debian.org/debian sid/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:35 http://deb.debian.org/debian sid/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.20.0-1 [49.9 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:45 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:55 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.12.0+git20250209.89ed161+ds-1 [365 kB] Get:58 http://deb.debian.org/debian sid/main amd64 liberror-perl all 0.17029-2 [29.0 kB] Get:59 http://deb.debian.org/debian sid/main amd64 git-man all 1:2.47.2-0.1 [2205 kB] Get:60 http://deb.debian.org/debian sid/main amd64 git amd64 1:2.47.2-0.1 [8788 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:65 http://deb.debian.org/debian sid/main amd64 python3-attr all 25.1.0-1 [68.7 kB] Get:66 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:67 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get:68 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:69 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:70 http://deb.debian.org/debian sid/main amd64 python3-configargparse all 1.7-2 [31.4 kB] Get:71 http://deb.debian.org/debian sid/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get:72 http://deb.debian.org/debian sid/main amd64 python3-datrie amd64 0.8.2-5+b1 [174 kB] Get:73 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:74 http://deb.debian.org/debian sid/main amd64 python3-roman all 5.0-1 [10.6 kB] Get:75 http://deb.debian.org/debian sid/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:76 http://deb.debian.org/debian sid/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get:77 http://deb.debian.org/debian sid/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get:78 http://deb.debian.org/debian sid/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get:79 http://deb.debian.org/debian sid/main amd64 python3-gitdb all 4.0.11-1 [45.5 kB] Get:80 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:81 http://deb.debian.org/debian sid/main amd64 python3-git all 3.1.37-3 [137 kB] Get:82 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get:83 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.10-1 [42.0 kB] Get:84 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:85 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:86 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:87 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:88 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:89 http://deb.debian.org/debian sid/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get:90 http://deb.debian.org/debian sid/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get:91 http://deb.debian.org/debian sid/main amd64 python3-rpds-py amd64 0.21.0-2 [287 kB] Get:92 http://deb.debian.org/debian sid/main amd64 python3-referencing all 0.35.1-2 [23.5 kB] Get:93 http://deb.debian.org/debian sid/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get:94 http://deb.debian.org/debian sid/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get:95 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:96 http://deb.debian.org/debian sid/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get:97 http://deb.debian.org/debian sid/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get:98 http://deb.debian.org/debian sid/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get:99 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:100 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:101 http://deb.debian.org/debian sid/main amd64 python3-plac all 1.4.3-2 [65.7 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get:103 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-py all 1.11.0-4 [88.8 kB] Get:106 http://deb.debian.org/debian sid/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get:107 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get:108 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:109 http://deb.debian.org/debian sid/main amd64 python3-retry all 0.9.2-3 [7088 B] Get:110 http://deb.debian.org/debian sid/main amd64 python3-wrapt amd64 1.15.0-4 [43.5 kB] Get:111 http://deb.debian.org/debian sid/main amd64 python3-smart-open all 7.1.0-1 [98.7 kB] Get:112 http://deb.debian.org/debian sid/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get:113 http://deb.debian.org/debian sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get:114 http://deb.debian.org/debian sid/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get:115 http://deb.debian.org/debian sid/main amd64 python3-toposort all 1.10-2 [7336 B] Get:116 http://deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get:117 http://deb.debian.org/debian sid/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get:118 http://deb.debian.org/debian sid/main amd64 snakemake all 7.32.4-7 [318 kB] Preconfiguring packages ... Fetched 43.6 MB in 0s (143 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 ... 5027 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... 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_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... 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Selecting previously unselected package python3-requests. Preparing to unpack .../093-python3-requests_2.32.3+dfsg-1_all.deb ... Unpacking python3-requests (2.32.3+dfsg-1) ... Selecting previously unselected package python3-retry. Preparing to unpack .../094-python3-retry_0.9.2-3_all.deb ... Unpacking python3-retry (0.9.2-3) ... Selecting previously unselected package python3-wrapt. Preparing to unpack .../095-python3-wrapt_1.15.0-4_amd64.deb ... Unpacking python3-wrapt (1.15.0-4) ... Selecting previously unselected package python3-smart-open. Preparing to unpack .../096-python3-smart-open_7.1.0-1_all.deb ... Unpacking python3-smart-open (7.1.0-1) ... Selecting previously unselected package python3-stopit. Preparing to unpack .../097-python3-stopit_1.1.2-3_all.deb ... Unpacking python3-stopit (1.1.2-3) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../098-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package python3-throttler. Preparing to unpack .../099-python3-throttler_1.2.2-2_all.deb ... Unpacking python3-throttler (1.2.2-2) ... Selecting previously unselected package python3-toposort. Preparing to unpack .../100-python3-toposort_1.10-2_all.deb ... Unpacking python3-toposort (1.10-2) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../101-python3-yaml_6.0.2-1+b1_amd64.deb ... Unpacking python3-yaml (6.0.2-1+b1) ... Selecting previously unselected package python3-yte. Preparing to unpack .../102-python3-yte_1.5.4-1_all.deb ... Unpacking python3-yte (1.5.4-1) ... Selecting previously unselected package snakemake. Preparing to unpack .../103-snakemake_7.32.4-7_all.deb ... Unpacking snakemake (7.32.4-7) ... Setting up media-types (11.0.0) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunistring5:amd64 (1.3-1) ... Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up libtasn1-6:amd64 (4.20.0-1) ... Setting up git-man (1:2.47.2-0.1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.4.0-2) ... Setting up readline-common (8.2-6) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.11+ds-3) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up python3.13 (3.13.2-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-plac (1.4.3-2) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up liberror-perl (0.17029-2) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2024.12.14+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up coinor-libclp1:amd64 (1.17.10+ds-1) ... Setting up python3-dpath (2.2.0-1) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-idna (3.10-1) ... Setting up python3-wrapt (1.15.0-4) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-rpds-py (0.21.0-2) ... Setting up python3-fastjsonschema (2.21.1-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up coinor-libcgl1:amd64 (0.60.9+ds-1) ... Setting up python3-datrie:amd64 (0.8.2-5+b1) ... Setting up python3-smmap (6.0.0-1) ... Setting up python3-jupyter-core (5.7.2-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up python3-toposort (1.10-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-configargparse (1.7-2) ... Setting up python3-attr (25.1.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-smart-open (7.1.0-1) ... Setting up python3-py (1.11.0-4) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up libcurl3t64-gnutls:amd64 (8.12.0+git20250209.89ed161+ds-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up python3-gitdb (4.0.11-1) ... Setting up python3-yte (1.5.4-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Setting up python3-retry (0.9.2-3) ... Setting up git (1:2.47.2-0.1) ... Setting up python3-referencing (0.35.1-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up coinor-cbc (2.10.12+ds-1) ... Setting up python3-git (3.1.37-3) ... Setting up python3-stopit (1.1.2-3) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-pulp (2.7.0+dfsg-4) ... /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:322: SyntaxWarning: invalid escape sequence '\ ' """ Setting up python3-jsonschema (4.19.2-6) ... Setting up python3-nbformat (5.9.1-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up snakemake (7.32.4-7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', '-y', 'install', 'snakemake=7.32.4-7'] 0m31.8s INFO: Running scripts post_install 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_install_exceptions'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_install_exceptions'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_install_log_alternatives'] 0m31.9s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=snakemake=7.32.4-7: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=snakemake=7.32.4-7: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=snakemake=7.32.4-7: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=perl: piuparts=snakemake=7.32.4-7: /usr/bin/update-alternatives --remove rename /usr/bin/prename 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_install_log_alternatives'] 0m31.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m32.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m33.7s DEBUG: No broken symlinks as far as we can find. 0m34.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', '-ac', '--ignore-obsolete'] 0m35.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', '-ac', '--ignore-obsolete'] 0m35.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m35.7s DUMP: 0.15.6 0m35.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m35.7s INFO: Running adequate version 0.15.6 now. 0m35.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'snakemake'] 0m35.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'snakemake'] 0m35.8s INFO: Running scripts pre_remove 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_exceptions'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/pre_remove_exceptions'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.9s DUMP: install ok installed apt apt 2.9.28 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 1:2.40.4-3 install ok installed ca-certificates ca-certificates 20241223 install ok installed coinor-cbc coinor-cbc 2.10.12+ds-1 install ok installed coinor-libcbc3.1:amd64 coinor-libcbc3.1 2.10.12+ds-1 install ok installed coinor-libcgl1:amd64 coinor-libcgl1 0.60.9+ds-1 install ok installed coinor-libclp1:amd64 coinor-libclp1 1.17.10+ds-1 install ok installed coinor-libcoinutils3v5:amd64 coinor-libcoinutils3v5 2.11.11+ds-3 install ok installed coinor-libosi1v5:amd64 coinor-libosi1v5 0.108.10+ds-1+b1 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 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 docutils-common docutils-common 0.21.2+dfsg-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed fonts-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-16 install ok installed git git 1:2.47.2-0.1 install ok installed git-man git-man 1:2.47.2-0.1 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 2.9.28 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 2.40.4-3 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 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 8.12.0+git20250209.89ed161+ds-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+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 liberror-perl liberror-perl 0.17029-2 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 libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-16 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 libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 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 libldap2:amd64 libldap2 2.6.9+dfsg-1 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 2.40.4-3 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 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 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 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 3.13.2-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.2-1 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 3.8-1 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 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-3 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 4.20.0-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250125-2 install ok installed libudev1:amd64 libudev1 257.2-3 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-3 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 1.3.4.20250131-1 install ok installed media-types media-types 11.0.0 install ok installed mount mount 2.40.4-3 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 openssl 3.4.0-2 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 perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed python3 python3 3.13.1-2 install ok installed python3-attr python3-attr 25.1.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-certifi python3-certifi 2024.12.14+ds-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.0-1+b1 install ok installed python3-configargparse python3-configargparse 1.7-2 install ok installed python3-connection-pool python3-connection-pool 0.0.3-2 install ok installed python3-datrie:amd64 python3-datrie 0.8.2-5+b1 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-docutils python3-docutils 0.21.2+dfsg-2 install ok installed python3-dpath python3-dpath 2.2.0-1 install ok installed python3-fastjsonschema python3-fastjsonschema 2.21.1-1 install ok installed python3-git python3-git 3.1.37-3 install ok installed python3-gitdb python3-gitdb 4.0.11-1 install ok installed python3-humanfriendly python3-humanfriendly 10.0-6 install ok installed python3-idna python3-idna 3.10-1 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-jinja2 python3-jinja2 3.1.5-2 install ok installed python3-jsonschema python3-jsonschema 4.19.2-6 install ok installed python3-jsonschema-specifications python3-jsonschema-specifications 2023.12.1-2 install ok installed python3-jupyter-core python3-jupyter-core 5.7.2-5 install ok installed python3-markupsafe python3-markupsafe 2.1.5-1+b2 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-nbformat python3-nbformat 5.9.1-1 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pkg-resources python3-pkg-resources 75.6.0-1 install ok installed python3-plac python3-plac 1.4.3-2 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-psutil python3-psutil 5.9.8-2 install ok installed python3-pulp python3-pulp 2.7.0+dfsg-4 install ok installed python3-py python3-py 1.11.0-4 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-ratelimiter python3-ratelimiter 1.2.0.post0-4 install ok installed python3-referencing python3-referencing 0.35.1-2 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-retry python3-retry 0.9.2-3 install ok installed python3-roman python3-roman 5.0-1 install ok installed python3-rpds-py python3-rpds-py 0.21.0-2 install ok installed python3-smart-open python3-smart-open 7.1.0-1 install ok installed python3-smmap python3-smmap 6.0.0-1 install ok installed python3-stopit python3-stopit 1.1.2-3 install ok installed python3-tabulate python3-tabulate 0.9.0-1 install ok installed python3-throttler python3-throttler 1.2.2-2 install ok installed python3-toposort python3-toposort 1.10-2 install ok installed python3-traitlets python3-traitlets 5.14.3+really5.14.3-1 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-urllib3 python3-urllib3 2.3.0-1 install ok installed python3-wrapt python3-wrapt 1.15.0-4 install ok installed python3-yaml python3-yaml 6.0.2-1+b1 install ok installed python3-yte python3-yte 1.5.4-1 install ok installed python3.13 python3.13 3.13.2-1 install ok installed python3.13-minimal python3.13-minimal 3.13.2-1 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 snakemake snakemake 7.32.4-7 install ok installed sqv sqv 1.2.1-6 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 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-3 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'remove', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fonts-glyphicons-halflings', 'git', 'git-man', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdatrie1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libidn2-0:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-attr', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-markupsafe', 'python3-minimal', 'python3-more-itertools', 'python3-nbformat', 'python3-packaging', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-roman', 'python3-rpds-py', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-tabulate', 'python3-throttler', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'xml-core', 'snakemake'] 0m44.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common fonts-glyphicons-halflings git git-man libblas3 libbrotli1 libcurl3t64-gnutls libdatrie1 liberror-perl libexpat1 libffi8 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgnutls30t64 libgssapi-krb5-2 libidn2-0 libjs-bootstrap libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libperl5.40 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtasn1-6 libunistring5 libyaml-0-2 media-types netbase openssl perl perl-modules-5.40 python3 python3-attr python3-autocommand python3-certifi python3-chardet python3-charset-normalizer python3-configargparse python3-connection-pool python3-datrie python3-decorator python3-docutils python3-dpath python3-fastjsonschema python3-git python3-gitdb python3-humanfriendly python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-markupsafe python3-minimal python3-more-itertools python3-nbformat python3-packaging python3-pkg-resources python3-plac python3-platformdirs python3-psutil python3-pulp python3-py python3-pyparsing python3-ratelimiter python3-referencing python3-requests python3-retry python3-roman python3-rpds-py python3-smart-open python3-smmap python3-stopit python3-tabulate python3-throttler python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-urllib3 python3-wrapt python3-yaml python3-yte python3.13 python3.13-minimal readline-common sgml-base snakemake xml-core 0 upgraded, 0 newly installed, 118 to remove and 0 not upgraded. After this operation, 190 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 ... 12246 files and directories currently installed.) Removing snakemake (7.32.4-7) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing python3-pulp (2.7.0+dfsg-4) ... Removing coinor-cbc (2.10.12+ds-1) ... Removing coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Removing coinor-libcgl1:amd64 (0.60.9+ds-1) ... Removing coinor-libclp1:amd64 (1.17.10+ds-1) ... Removing coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Removing coinor-libcoinutils3v5:amd64 (2.11.11+ds-3) ... Removing python3-docutils (0.21.2+dfsg-2) ... Removing docutils-common (0.21.2+dfsg-2) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing python3-git (3.1.37-3) ... Removing git (1:2.47.2-0.1) ... Removing git-man (1:2.47.2-0.1) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing libcurl3t64-gnutls:amd64 (8.12.0+git20250209.89ed161+ds-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing python3-datrie:amd64 (0.8.2-5+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing liberror-perl (0.17029-2) ... Removing python3-nbformat (5.9.1-1) ... Removing python3-jsonschema (4.19.2-6) ... Removing python3-jsonschema-specifications (2023.12.1-2) ... Removing python3-referencing (0.35.1-2) ... Removing python3-rpds-py (0.21.0-2) ... Removing python3-yte (1.5.4-1) ... Removing python3-stopit (1.1.2-3) ... Removing python3-pkg-resources (75.6.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing python3-humanfriendly (10.0-6) ... Removing python3-yaml (6.0.2-1+b1) ... Removing python3-jupyter-core (5.7.2-5) ... Removing python3-traitlets (5.14.3+really5.14.3-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-16) ... Removing libgssapi-krb5-2:amd64 (1.21.3-4) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... 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 libldap2:amd64 (2.6.9+dfsg-1) ... 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 libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libyaml-0-2:amd64 (0.2.5-2) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing python3-attr (25.1.0-1) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-certifi (2024.12.14+ds-1) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-charset-normalizer (3.4.0-1+b1) ... Removing python3-configargparse (1.7-2) ... Removing python3-connection-pool (0.0.3-2) ... Removing python3-retry (0.9.2-3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-dpath (2.2.0-1) ... Removing python3-fastjsonschema (2.21.1-1) ... Removing python3-gitdb (4.0.11-1) ... Removing python3-idna (3.10-1) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-jinja2 (3.1.5-2) ... Removing python3-markupsafe (2.1.5-1+b2) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-packaging (24.2-1) ... Removing python3-plac (1.4.3-2) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-psutil (5.9.8-2) ... Removing python3-py (1.11.0-4) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-ratelimiter (1.2.0.post0-4) ... Removing python3-roman (5.0-1) ... Removing python3-smart-open (7.1.0-1) ... Removing python3-smmap (6.0.0-1) ... Removing python3-tabulate (0.9.0-1) ... Removing python3-throttler (1.2.2-2) ... Removing python3-toposort (1.10-2) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3-urllib3 (2.3.0-1) ... Removing python3-wrapt (1.15.0-4) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3 (3.13.1-2) ... Removing python3.13 (3.13.2-1) ... Removing python3-minimal (3.13.1-2) ... Removing python3.13-minimal (3.13.2-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.13.1-2) ... Removing libpython3.13-stdlib:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libgnutls30t64:amd64 (3.8.8-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libffi8:amd64 (3.4.6-1) ... Removing libidn2-0:amd64 (2.3.7-2+b1) ... Removing libncursesw6:amd64 (6.5+20250125-2) ... Removing libpython3.13-minimal:amd64 (3.13.2-1) ... 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 libtasn1-6:amd64 (4.20.0-1) ... Removing libunistring5:amd64 (1.3-1) ... Removing media-types (11.0.0) ... Removing netbase (6.4) ... Removing openssl (3.4.0-2) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-6) ... 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'remove', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fonts-glyphicons-halflings', 'git', 'git-man', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdatrie1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libidn2-0:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-attr', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-markupsafe', 'python3-minimal', 'python3-more-itertools', 'python3-nbformat', 'python3-packaging', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-roman', 'python3-rpds-py', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-tabulate', 'python3-throttler', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'xml-core', 'snakemake'] 0m44.5s INFO: Running scripts post_remove 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_remove_exceptions'] 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_remove_exceptions'] 0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--purge', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fonts-glyphicons-halflings', 'git', 'git-man', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdatrie1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libidn2-0:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-attr', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-markupsafe', 'python3-minimal', 'python3-more-itertools', 'python3-nbformat', 'python3-packaging', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-roman', 'python3-rpds-py', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-tabulate', 'python3-throttler', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'xml-core'] 0m44.8s DUMP: (Reading database ... 5046 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove coinor-cbc which isn't installed dpkg: warning: ignoring request to remove coinor-libcbc3.1 which isn't installed dpkg: warning: ignoring request to remove coinor-libcgl1 which isn't installed dpkg: warning: ignoring request to remove coinor-libclp1 which isn't installed dpkg: warning: ignoring request to remove coinor-libcoinutils3v5 which isn't installed dpkg: warning: ignoring request to remove coinor-libosi1v5 which isn't installed Purging configuration files for docutils-common (0.21.2+dfsg-2) ... dpkg: warning: ignoring request to remove fonts-glyphicons-halflings which isn't installed Purging configuration files for git (1:2.47.2-0.1) ... dpkg: warning: ignoring request to remove git-man 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 libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove liberror-perl 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 libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-4) ... dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libjs-bootstrap which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 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 libldap2 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 libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 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 (3.13.2-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib 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 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 libunistring5 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (11.0.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.4.0-2) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed 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-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-configargparse which isn't installed dpkg: warning: ignoring request to remove python3-connection-pool which isn't installed dpkg: warning: ignoring request to remove python3-datrie which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-docutils which isn't installed dpkg: warning: ignoring request to remove python3-dpath which isn't installed dpkg: warning: ignoring request to remove python3-fastjsonschema which isn't installed dpkg: warning: ignoring request to remove python3-git which isn't installed dpkg: warning: ignoring request to remove python3-gitdb which isn't installed dpkg: warning: ignoring request to remove python3-humanfriendly which isn't installed dpkg: warning: ignoring request to remove python3-idna 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-jinja2 which isn't installed Purging configuration files for python3-jsonschema (4.19.2-6) ... dpkg: warning: ignoring request to remove python3-jsonschema-specifications which isn't installed dpkg: warning: ignoring request to remove python3-jupyter-core which isn't installed dpkg: warning: ignoring request to remove python3-markupsafe 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-nbformat which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-plac which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-psutil which isn't installed dpkg: warning: ignoring request to remove python3-pulp which isn't installed dpkg: warning: ignoring request to remove python3-py which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-ratelimiter which isn't installed dpkg: warning: ignoring request to remove python3-referencing which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-retry which isn't installed dpkg: warning: ignoring request to remove python3-roman which isn't installed dpkg: warning: ignoring request to remove python3-rpds-py which isn't installed dpkg: warning: ignoring request to remove python3-smart-open which isn't installed dpkg: warning: ignoring request to remove python3-smmap which isn't installed dpkg: warning: ignoring request to remove python3-stopit which isn't installed dpkg: warning: ignoring request to remove python3-tabulate which isn't installed dpkg: warning: ignoring request to remove python3-throttler which isn't installed dpkg: warning: ignoring request to remove python3-toposort which isn't installed dpkg: warning: ignoring request to remove python3-traitlets 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-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wrapt which isn't installed dpkg: warning: ignoring request to remove python3-yaml which isn't installed dpkg: warning: ignoring request to remove python3-yte which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.2-1) ... Purging configuration files for readline-common (8.2-6) ... Purging configuration files for sgml-base (1.31) ... Purging configuration files for xml-core (0.19) ... 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--purge', 'ca-certificates', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'docutils-common', 'fonts-glyphicons-halflings', 'git', 'git-man', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdatrie1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libffi8:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libidn2-0:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-attr', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-configargparse', 'python3-connection-pool', 'python3-datrie:amd64', 'python3-decorator', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-git', 'python3-gitdb', 'python3-humanfriendly', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-markupsafe', 'python3-minimal', 'python3-more-itertools', 'python3-nbformat', 'python3-packaging', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-pyparsing', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-roman', 'python3-rpds-py', 'python3-smart-open', 'python3-smmap', 'python3-stopit', 'python3-tabulate', 'python3-throttler', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3-wrapt', 'python3-yaml', 'python3-yte', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'xml-core'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--purge', 'snakemake'] 0m44.8s DUMP: dpkg: warning: ignoring request to remove snakemake which isn't installed 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--purge', 'snakemake'] 0m44.8s INFO: Running scripts post_purge 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_purge_exceptions'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_purge_exceptions'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--purge', '--pending'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--purge', '--pending'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--remove', '--pending'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg', '--remove', '--pending'] 0m44.8s INFO: Running scripts post_test 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_test_exceptions'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'tmp/scripts/post_test_exceptions'] 0m44.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m45.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m45.6s DEBUG: No broken symlinks as far as we can find. 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-divert', '--list'] 0m45.6s 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 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'dpkg-divert', '--list'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'clean'] 0m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi', 'apt-get', 'clean'] 0m45.7s DEBUG: Recording chroot state 0m46.2s INFO: PASS: Installation and purging test. 0m46.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/shm'] 0m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/shm'] 0m46.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/console'] 0m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/console'] 0m46.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/ptmx'] 0m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/ptmx'] 0m46.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/pts'] 0m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/dev/pts'] 0m46.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/proc'] 0m46.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi/proc'] 0m46.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m46.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp7_ah5bgi'] 0m46.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp7_ah5bgi 0m46.7s INFO: PASS: All tests. 0m46.7s INFO: piuparts run ends. ret=0 End: 2025-02-10 03:40:08 GMT