Start: 2024-10-08 03:47:16 GMT [testing] Package: snakemake Version: 7.32.4-5 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-pkg-resources, 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_7.32.4-5_all.deb Size: 317612 MD5sum: 0d83b817f9867fb0b48dda942c1342cf SHA256: 5c526e9e0c7be3cd1be60cd639cf6a30734df07bb13ca664e488667b59f9d09d [sid] Package: snakemake Version: 7.32.4-6 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_7.32.4-6_all.deb Size: 317740 MD5sum: c4f3069605b9fac5585052b0a16b15fe SHA256: b65a3649d32e7ea3ae5fb9876de196d6bd0573589bff2649748b0c596ba314e0 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt snakemake=7.32.4-6 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt snakemake=7.32.4-6 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/tmpf3b1da39 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpf3b1da39 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpf3b1da39/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', 'update'] 0m2.9s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [169 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9317 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6215 kB] Fetched 15.7 MB in 2s (8366 kB/s) Reading package lists... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', 'update'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s DUMP: 8f1478ca063948284943db6823b5e4ef - 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s INFO: Running scripts post_setup 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s 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 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.9s 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' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b1 install ok installed bsdutils bsdutils 1:2.40.2-8 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-3 install ok installed gpgv gpgv 2.2.43-8+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-8 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 2.40-2 install ok installed libc6:amd64 libc6 2.40-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-8 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-8 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 256.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.6-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-8 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-8 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.38.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-8 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m5.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m5.2s INFO: Running scripts is_testable 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s INFO: Running scripts pre_test 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_test_root_password'] 0m5.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_test_root_password'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'show', '--no-all-versions', 'snakemake'] 0m5.4s DUMP: Package: snakemake Version: 7.32.4-5 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-pkg-resources, 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-en: pythonic workflow management system Build systems like GNU Make are frequently used to create complicated workflows, e.g. in bioinformatics. This project aims to reduce the complexity of creating workflows by providing a clean and modern domain specific language (DSL) in Python style, together with a fast and comfortable execution environment. Description-md5: 7f9c57469c639aa1e67301b2a7ed865e Homepage: https://snakemake.readthedocs.io/ Section: science Priority: optional Filename: pool/main/s/snakemake/snakemake_7.32.4-5_all.deb Size: 317612 MD5sum: 0d83b817f9867fb0b48dda942c1342cf SHA256: 5c526e9e0c7be3cd1be60cd639cf6a30734df07bb13ca664e488667b59f9d09d 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'show', '--no-all-versions', 'snakemake'] 0m5.4s INFO: apt-cache knows about the following packages: snakemake 0m5.4s INFO: Running scripts pre_install 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_database-server'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_database-server'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_exceptions'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_exceptions'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_extras'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_extras'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy'] 0m5.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy', 'snakemake'] 0m5.6s DUMP: snakemake: Installed: (none) Candidate: 7.32.4-5 Version table: 7.32.4-5 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy', 'snakemake'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-y', 'install', 'snakemake'] 0m25.0s DUMP: Reading package lists... Building dependency tree... 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 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgssapi-krb5-2 libjs-bootstrap libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libperl5.38t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtirpc-common libtirpc3t64 libyaml-0-2 media-types netbase openssl perl perl-modules-5.38 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 python3.12 python3.12-minimal readline-common sgml-base xml-core Suggested packages: gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn gdbm-l10n 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 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 python3.12-venv python3.12-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-json-pointer 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 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgssapi-krb5-2 libjs-bootstrap libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libperl5.38t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtirpc-common libtirpc3t64 libyaml-0-2 media-types netbase openssl perl perl-modules-5.38 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 python3.12 python3.12-minimal readline-common sgml-base snakemake xml-core 0 upgraded, 115 newly installed, 0 to remove and 0 not upgraded. Need to get 40.3 MB of archives. After this operation, 179 MB of additional disk space will be used. 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Get:12 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:16 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.0-1 [902 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:27 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 coinor-libcoinutils3v5 amd64 2.11.4+repack1-4 [448 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-1 [280 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:54 http://deb.debian.org/debian 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python3-retry all 0.9.2-3 [7088 B] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-wrapt amd64 1.15.0-3 [43.3 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-smart-open all 7.0.4-2 [83.3 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-toposort all 1.10-2 [7336 B] Get:113 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1 [134 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-5 [318 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.3 MB in 0s (111 MB/s) Selecting previously unselected package perl-modules-5.38. (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 ... 5145 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.38_5.38.2-5_all.deb ... Unpacking perl-modules-5.38 (5.38.2-5) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. 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Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7482 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... 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Preparing to unpack .../83-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package python3-throttler. Preparing to unpack .../84-python3-throttler_1.2.2-2_all.deb ... Unpacking python3-throttler (1.2.2-2) ... Selecting previously unselected package python3-toposort. Preparing to unpack .../85-python3-toposort_1.10-2_all.deb ... Unpacking python3-toposort (1.10-2) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../86-python3-yaml_6.0.2-1_amd64.deb ... Unpacking python3-yaml (6.0.2-1) ... Selecting previously unselected package python3-yte. Preparing to unpack .../87-python3-yte_1.5.4-1_all.deb ... Unpacking python3-yte (1.5.4-1) ... Selecting previously unselected package snakemake. Preparing to unpack .../88-snakemake_7.32.4-5_all.deb ... Unpacking snakemake (7.32.4-5) ... Setting up media-types (10.1.0) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libsqlite3-0:amd64 (3.46.0-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up libblas3:amd64 (3.12.0-3) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up perl-modules-5.38 (5.38.2-5) ... Setting up libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up git-man (1:2.45.2-1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libperl5.38t64:amd64 (5.38.2-5) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-1) ... Setting up readline-common (8.2-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.4+repack1-4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.38.2-5) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up xml-core (0.19) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-1) ... Setting up liberror-perl (0.17029-2) ... Setting up coinor-libclp1:amd64 (1.17.10+ds-1) ... Setting up git (1:2.45.2-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up coinor-libcgl1:amd64 (0.60.9+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up python3-plac (1.4.1-1) ... 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 python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up coinor-cbc (2.10.12+ds-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-5) ... Setting up python3-certifi (2024.8.30-1) ... Setting up python3-dpath (2.2.0-1) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-idna (3.8-2) ... Setting up python3-wrapt (1.15.0-3) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-rpds-py (0.12.0-3+b1) ... Setting up python3-fastjsonschema (2.20.0-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up python3-datrie:amd64 (0.8.2-5) ... Setting up python3-smmap (6.0.0-1) ... Setting up python3-jupyter-core (5.7.2-4) ... Setting up python3-toposort (1.10-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-configargparse (1.7-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-smart-open (7.0.4-2) ... Setting up python3-jaraco.context (6.0.0-1) ... 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-charset-normalizer (3.3.2-4) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-yaml (6.0.2-1) ... 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-git (3.1.37-3) ... Setting up python3-referencing (0.35.1-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-py (1.11.0-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-retry (0.9.2-3) ... Setting up python3-stopit (1.1.2-3) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-jsonschema (4.19.2-4) ... Setting up python3-nbformat (5.9.1-1) ... Processing triggers for libc-bin (2.40-2) ... 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 (7.32.4-5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-y', 'install', 'snakemake'] 0m25.0s INFO: Running scripts post_install 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_install_exceptions'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_install_exceptions'] 0m25.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m25.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m25.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpf3b1da39 to sid 0m25.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m25.6s INFO: Running scripts pre_distupgrade 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', 'update'] 0m28.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9997 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7330 kB] Fetched 17.5 MB in 2s (7791 kB/s) Reading package lists... 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', 'update'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-yf', 'dist-upgrade'] 0m35.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils gcc-14-base gpgv libaudit-common libaudit1 libblkid1 libc-bin libc6 libgcc-s1 libgfortran5 libmount1 libpython3.12-minimal libpython3.12-stdlib libsmartcols1 libsqlite3-0 libstdc++6 libuuid1 login mount python3-attr python3-certifi python3-humanfriendly python3.12 python3.12-minimal snakemake tzdata util-linux 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 14.7 MB of archives. After this operation, 130 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-9 [105 kB] Get:2 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-6 [46.7 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-6 [72.8 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-6 [836 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-6 [715 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-3 [2807 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-9 [35.6 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-9 [168 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-9 [199 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-9 [139 kB] Get:11 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-9 [1216 kB] Get:12 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-9 [154 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-3 [627 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-1 [12.3 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-1 [54.5 kB] Get:16 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-9 [81.4 kB] Get:17 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.7-1 [671 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.7-1 [2162 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.7-1 [1965 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.7-1 [814 kB] Get:21 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-3 [255 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:23 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.44-1 [218 kB] Get:24 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:26 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get:27 http://deb.debian.org/debian sid/main amd64 snakemake all 7.32.4-6 [318 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.7 MB in 0s (127 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12053 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-9_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-9) over (2.40.2-8) ... Setting up libsmartcols1:amd64 (2.40.2-9) ... (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 ... 12053 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-9_amd64.deb ... Unpacking util-linux (2.40.2-9) over (2.40.2-8) ... Setting up util-linux (2.40.2-9) ... (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 ... 12053 files and directories currently installed.) Preparing to unpack .../mount_2.40.2-9_amd64.deb ... Unpacking mount (2.40.2-9) over (2.40.2-8) ... Preparing to unpack .../libc-bin_2.40-3_amd64.deb ... Unpacking libc-bin (2.40-3) over (2.40-2) ... Setting up libc-bin (2.40-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12053 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.0.1-1_all.deb ... Unpacking libaudit-common (1:4.0.1-1) over (1:3.1.2-4) ... Setting up libaudit-common (1:4.0.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12053 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.1-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.1-1) over (1:3.1.2-4+b1) ... Setting up libaudit1:amd64 (1:4.0.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12052 files and directories currently installed.) Preparing to unpack .../0-login_1%3a4.16.0-2+really2.40.2-9_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-9) over (1:4.16.0-2+really2.40.2-8) ... Preparing to unpack .../1-python3.12_3.12.7-1_amd64.deb ... Unpacking python3.12 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../2-python3.12-minimal_3.12.7-1_amd64.deb ... Unpacking python3.12-minimal (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../3-libpython3.12-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../4-libpython3.12-minimal_3.12.7-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-1) over (3.12.6-1) ... Preparing to unpack .../5-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) over (2024a-4) ... Preparing to unpack .../6-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) over (3.46.0-1) ... Preparing to unpack .../7-gpgv_2.2.44-1_amd64.deb ... Unpacking gpgv (2.2.44-1) over (2.2.43-8+b1) ... Setting up gpgv (2.2.44-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12039 files and directories currently installed.) Preparing to unpack .../python3-attr_24.2.0-1_all.deb ... Unpacking python3-attr (24.2.0-1) over (23.2.0-2) ... Preparing to unpack .../python3-certifi_2024.8.30+dfsg-1_all.deb ... Unpacking python3-certifi (2024.8.30+dfsg-1) over (2024.8.30-1) ... Preparing to unpack .../python3-humanfriendly_10.0-6_all.deb ... Unpacking python3-humanfriendly (10.0-6) over (10.0-5) ... Preparing to unpack .../snakemake_7.32.4-6_all.deb ... Unpacking snakemake (7.32.4-6) over (7.32.4-5) ... Setting up python3-attr (24.2.0-1) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libpython3.12-minimal:amd64 (3.12.7-1) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 8 03:47:50 UTC 2024. Universal Time is now: Tue Oct 8 03:47:50 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up libgfortran5:amd64 (14.2.0-6) ... Setting up mount (2.40.2-9) ... Setting up login (1:4.16.0-2+really2.40.2-9) ... Setting up python3.12-minimal (3.12.7-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-1) ... Setting up python3.12 (3.12.7-1) ... Setting up snakemake (7.32.4-6) ... Processing triggers for libc-bin (2.40-3) ... 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-yf', 'dist-upgrade'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m35.6s DUMP: cb54e2e86f3db98e774b0bcf4cc688c5 - 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'show', '--no-all-versions', 'snakemake'] 0m35.8s DUMP: Package: snakemake Version: 7.32.4-6 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-en: pythonic workflow management system Build systems like GNU Make are frequently used to create complicated workflows, e.g. in bioinformatics. This project aims to reduce the complexity of creating workflows by providing a clean and modern domain specific language (DSL) in Python style, together with a fast and comfortable execution environment. Description-md5: 7f9c57469c639aa1e67301b2a7ed865e Homepage: https://snakemake.readthedocs.io/ Section: science Priority: optional Filename: pool/main/s/snakemake/snakemake_7.32.4-6_all.deb Size: 317740 MD5sum: c4f3069605b9fac5585052b0a16b15fe SHA256: b65a3649d32e7ea3ae5fb9876de196d6bd0573589bff2649748b0c596ba314e0 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'show', '--no-all-versions', 'snakemake'] 0m35.8s INFO: apt-cache knows about the following packages: snakemake 0m35.8s INFO: Running scripts pre_install 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_database-server'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_database-server'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_exceptions'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_exceptions'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_extras'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_extras'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy'] 0m36.0s 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: 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy', 'snakemake'] 0m36.0s DUMP: snakemake: Installed: 7.32.4-6 Candidate: 7.32.4-6 Version table: *** 7.32.4-6 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy', 'snakemake'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-y', 'install', 'snakemake'] 0m36.5s DUMP: Reading package lists... Building dependency tree... Reading state information... snakemake is already the newest version (7.32.4-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m36.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-y', 'install', 'snakemake'] 0m36.5s INFO: Running scripts post_install 0m36.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_install_exceptions'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_install_exceptions'] 0m36.6s INFO: Running scripts post_distupgrade 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_exceptions'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_exceptions'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_zz_backports'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_distupgrade_zz_backports'] 0m36.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m37.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m37.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m38.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m38.0s INFO: Running scripts pre_install 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_database-server'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_database-server'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_exceptions'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_exceptions'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_extras'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_extras'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy'] 0m38.1s 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: 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy', 'snakemake'] 0m38.1s DUMP: snakemake: Installed: 7.32.4-6 Candidate: 7.32.4-6 Version table: *** 7.32.4-6 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-cache', 'policy', 'snakemake'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-y', 'install', 'snakemake=7.32.4-6'] 0m38.6s DUMP: Reading package lists... Building dependency tree... Reading state information... snakemake is already the newest version (7.32.4-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', '-y', 'install', 'snakemake=7.32.4-6'] 0m38.6s INFO: Running scripts post_install 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_install_exceptions'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_install_exceptions'] 0m38.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m39.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m39.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '-ac', '--ignore-obsolete'] 0m41.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '-ac', '--ignore-obsolete'] 0m41.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m41.0s DUMP: 0.15.6 0m41.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m41.0s INFO: Running adequate version 0.15.6 now. 0m41.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'snakemake'] 0m41.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'snakemake'] 0m41.2s INFO: Running scripts pre_remove 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_exceptions'] 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/pre_remove_exceptions'] 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.7s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b1 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed ca-certificates ca-certificates 20240203 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 2.11.4+repack1-4 install ok installed coinor-libosi1v5:amd64 coinor-libosi1v5 0.108.10+ds-1 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed docutils-common docutils-common 0.21.2+dfsg-2 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 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 14.2.0-6 install ok installed git git 1:2.45.2-1 install ok installed git-man git-man 1:2.45.2-1 install ok installed gpgv gpgv 2.2.44-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 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 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.10.1-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed liberror-perl liberror-perl 0.17029-2 install ok installed libexpat1:amd64 libexpat1 2.6.3-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 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 14.2.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 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 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.63.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-5 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-7 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 256.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libudev1:amd64 libudev1 256.6-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.2-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.38.2-5 install ok installed perl-base perl-base 5.38.2-5 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-5 install ok installed python3 python3 3.12.6-1 install ok installed python3-attr python3-attr 24.2.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-certifi python3-certifi 2024.8.30+dfsg-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.3.2-4 install ok installed python3-configargparse python3-configargparse 1.7-1 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 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 2.20.0-1 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 3.8-2 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 3.1.3-1 install ok installed python3-jsonschema python3-jsonschema 4.19.2-4 install ok installed python3-jsonschema-specifications python3-jsonschema-specifications 2023.12.1-2 install ok installed python3-jupyter-core python3-jupyter-core 5.7.2-4 install ok installed python3-markupsafe python3-markupsafe 2.1.5-1+b1 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-nbformat python3-nbformat 5.9.1-1 install ok installed python3-packaging python3-packaging 24.1-1 install ok installed python3-pkg-resources python3-pkg-resources 74.1.2-2 install ok installed python3-plac python3-plac 1.4.1-1 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 1.11.0-2 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 0.35.1-1 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 4.2-1 install ok installed python3-rpds-py python3-rpds-py 0.12.0-3+b1 install ok installed python3-smart-open python3-smart-open 7.0.4-2 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 4.3.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3-wrapt python3-wrapt 1.15.0-3 install ok installed python3-yaml python3-yaml 6.0.2-1 install ok installed python3-yte python3-yte 1.5.4-1 install ok installed python3.12 python3.12 3.12.7-1 install ok installed python3.12-minimal python3.12-minimal 3.12.7-1 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed snakemake snakemake 7.32.4-6 install ok installed sysvinit-utils sysvinit-utils 3.10-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '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', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.38', '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', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core', 'snakemake'] 0m48.4s 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 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgssapi-krb5-2 libjs-bootstrap libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libperl5.38t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtirpc-common libtirpc3t64 libyaml-0-2 media-types netbase openssl perl perl-modules-5.38 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 python3.12 python3.12-minimal readline-common sgml-base snakemake xml-core 0 upgraded, 0 newly installed, 115 to remove and 0 not upgraded. After this operation, 179 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 ... 12038 files and directories currently installed.) Removing snakemake (7.32.4-6) ... 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) ... Removing coinor-libcoinutils3v5:amd64 (2.11.4+repack1-4) ... 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 (1:2.45.2-1) ... Removing git-man (1:2.45.2-1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libcurl3t64-gnutls:amd64 (8.10.1-1) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing python3-datrie:amd64 (0.8.2-5) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing liberror-perl (0.17029-2) ... Removing python3-nbformat (5.9.1-1) ... Removing python3-jsonschema (4.19.2-4) ... Removing python3-jsonschema-specifications (2023.12.1-2) ... Removing python3-referencing (0.35.1-1) ... Removing python3-rpds-py (0.12.0-3+b1) ... Removing python3-yte (1.5.4-1) ... Removing python3-stopit (1.1.2-3) ... Removing python3-retry (0.9.2-3) ... Removing python3-py (1.11.0-2) ... Removing python3-humanfriendly (10.0-6) ... Removing python3-yaml (6.0.2-1) ... Removing python3-jupyter-core (5.7.2-4) ... Removing python3-traitlets (5.14.3+really5.14.3-1) ... Removing perl (5.38.2-5) ... Removing libperl5.38t64:amd64 (5.38.2-5) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-6) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Removing libnghttp2-14:amd64 (1.63.0-1) ... Removing libnghttp3-9:amd64 (1.4.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libssh2-1t64:amd64 (1.11.0-7) ... Removing libyaml-0-2:amd64 (0.2.5-1+b1) ... Removing perl-modules-5.38 (5.38.2-5) ... Removing python3-attr (24.2.0-1) ... Removing python3-certifi (2024.8.30+dfsg-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-charset-normalizer (3.3.2-4) ... Removing python3-configargparse (1.7-1) ... Removing python3-connection-pool (0.0.3-2) ... Removing python3-decorator (5.1.1-5) ... Removing python3-dpath (2.2.0-1) ... Removing python3-fastjsonschema (2.20.0-1) ... Removing python3-gitdb (4.0.11-1) ... Removing python3-idna (3.8-2) ... Removing python3-jinja2 (3.1.3-1) ... Removing python3-markupsafe (2.1.5-1+b1) ... Removing python3-packaging (24.1-1) ... Removing python3-plac (1.4.1-1) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-psutil (5.9.8-2) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-ratelimiter (1.2.0.post0-4) ... Removing python3-roman (4.2-1) ... Removing python3-smart-open (7.0.4-2) ... 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-urllib3 (2.0.7-2) ... Removing python3-wrapt (1.15.0-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-pkg-resources (74.1.2-2) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.3.0-1) ... Removing openssl (3.3.2-1) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3 (3.12.6-1) ... Removing python3.12 (3.12.7-1) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12-minimal (3.12.7-1) ... Removing libexpat1:amd64 (2.6.3-1) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2) ... Removing libpython3.12-minimal:amd64 (3.12.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... 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 libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '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', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.38', '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', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core', 'snakemake'] 0m48.4s INFO: Running scripts post_remove 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_remove_exceptions'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_remove_exceptions'] 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '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', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.38', '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', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core'] 0m48.6s DUMP: (Reading database ... 5152 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... 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 (1:2.45.2-1) ... 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 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 Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... 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 libldap-2.5-0 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 libnsl2 which isn't installed dpkg: warning: ignoring request to remove libperl5.38t64 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 libpython3.12-minimal:amd64 (3.12.7-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... 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 Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-1) ... Purging configuration files for perl (5.38.2-5) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for python3 (3.12.6-1) ... 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 (4.19.2-4) ... 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 python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-1) ... Purging configuration files for readline-common (8.2-5) ... Purging configuration files for sgml-base (1.31) ... Purging configuration files for xml-core (0.19) ... 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', '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', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libjs-bootstrap', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'perl', 'perl-modules-5.38', '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', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg', '--purge', 'snakemake'] 0m48.6s DUMP: dpkg: warning: ignoring request to remove snakemake which isn't installed 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg', '--purge', 'snakemake'] 0m48.6s INFO: Running scripts post_purge 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_purge_exceptions'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_purge_exceptions'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg', '--purge', '--pending'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg', '--purge', '--pending'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg', '--remove', '--pending'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg', '--remove', '--pending'] 0m48.7s INFO: Running scripts post_test 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_test_exceptions'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'tmp/scripts/post_test_exceptions'] 0m48.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m49.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg-divert', '--list'] 0m49.2s 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 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'dpkg-divert', '--list'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', 'clean'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf3b1da39', 'apt-get', 'clean'] 0m49.2s DEBUG: Recording chroot state 0m50.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/shm'] 0m50.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/shm'] 0m50.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/console'] 0m50.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/console'] 0m50.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/ptmx'] 0m50.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/ptmx'] 0m50.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/pts'] 0m50.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/dev/pts'] 0m50.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/proc'] 0m50.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf3b1da39/proc'] 0m50.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m50.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpf3b1da39'] 0m50.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpf3b1da39 0m50.3s INFO: PASS: Upgrading between Debian distributions. 0m50.3s INFO: PASS: All tests. 0m50.3s INFO: piuparts run ends. ret=0 End: 2024-10-08 03:48:07 GMT