Start: 2025-08-12 21:57:47 GMT [testing] Package: python3-cobra Source: python-cobra Version: 0.29.1-3 Installed-Size: 1878 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-3), python3-tabulate, python3-sbml5 Suggests: python3-matplotlib, qsopt-ex Description: constraint-based modeling of biological networks with Python 3 Homepage: https://opencobra.github.io/cobrapy/ Description-md5: 0052f98776eccb61924a15b5d6618e25 Section: python Priority: optional Filename: pool/main/p/python-cobra/python3-cobra_0.29.1-3_amd64.deb Size: 1119344 MD5sum: 18e670194f1ec471bc967eb5dc4a3e82 SHA256: 7afc9b545d203492f9017ca53552d392a612d4caa40678646889129b53b5663e [sid] Package: python3-cobra Source: python-cobra Version: 0.29.1-3 Installed-Size: 1878 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-3), python3-tabulate, python3-sbml5 Suggests: python3-matplotlib, qsopt-ex Description: constraint-based modeling of biological networks with Python 3 Homepage: https://opencobra.github.io/cobrapy/ Description-md5: 0052f98776eccb61924a15b5d6618e25 Section: python Priority: optional Filename: pool/main/p/python-cobra/python3-cobra_0.29.1-3_amd64.deb Size: 1119344 MD5sum: 18e670194f1ec471bc967eb5dc4a3e82 SHA256: 7afc9b545d203492f9017ca53552d392a612d4caa40678646889129b53b5663e Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-cobra=0.29.1-3 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 1.6.1~202508101417~1.6.0-7-g17c4ea32 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-cobra=0.29.1-3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp4_j4uh54 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp4_j4uh54 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp4_j4uh54/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'update'] 0m1.6s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [125 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9728 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6527 kB] Fetched 16.4 MB in 1s (17.7 MB/s) Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libaudit-common libaudit1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 72.9 kB of archives. After this operation, 27.6 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.0.5-1 [13.5 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.0.5-1 [59.4 kB] Fetched 72.9 kB in 0s (942 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4934 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.0.5-1_all.deb ... Unpacking libaudit-common (1:4.0.5-1) over (1:4.0.2-2) ... Setting up libaudit-common (1:4.0.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4934 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.5-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.5-1) over (1:4.0.2-2+b2) ... Setting up libaudit1:amd64 (1:4.0.5-1) ... Processing triggers for libc-bin (2.41-12) ... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s DUMP: a176e44298643052052b640cb3efe9ef - 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s INFO: Running scripts post_setup 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_dummy_users'] 0m2.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_dummy_users'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_forbid_home'] 0m2.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_forbid_home'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_minimize'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_minimize'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_zz_backports'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_setup_zz_backports'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.8s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.5-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.5-1 install ok installed libblkid1:amd64 libblkid1 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m3.1s INFO: Running scripts is_testable 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s INFO: Running scripts pre_test 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_test_root_password'] 0m3.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_test_root_password'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra'] 0m3.2s DUMP: Package: python3-cobra Source: python-cobra Version: 0.29.1-3 Installed-Size: 1878 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-3), python3-tabulate, python3-sbml5 Suggests: python3-matplotlib, qsopt-ex Description-en: constraint-based modeling of biological networks with Python 3 COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accommodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux balance analysis, flux variability analysis, and gene deletion analyses. Description-md5: 0052f98776eccb61924a15b5d6618e25 Homepage: https://opencobra.github.io/cobrapy/ Section: python Priority: optional Filename: pool/main/p/python-cobra/python3-cobra_0.29.1-3_amd64.deb Size: 1119344 MD5sum: 18e670194f1ec471bc967eb5dc4a3e82 SHA256: 7afc9b545d203492f9017ca53552d392a612d4caa40678646889129b53b5663e 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra'] 0m3.2s INFO: apt-cache knows about the following packages: python3-cobra 0m3.2s INFO: Running scripts pre_install 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_database-server'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_database-server'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_exceptions'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_exceptions'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_extras'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_extras'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy'] 0m3.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy', 'python3-cobra'] 0m3.2s DUMP: python3-cobra: Installed: (none) Candidate: 0.29.1-3 Version table: 0.29.1-3 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy', 'python3-cobra'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-y', 'install', 'python3-cobra'] 0m20.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5 libglpk40 libgomp1 liblapack3 libltdl7 libncursesw6 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsuitesparseconfig7 libxml2 media-types netbase openssl python-cobra-data python3 python3-annotated-types python3-anyio python3-certifi python3-click python3-dateutil python3-depinfo python3-diskcache python3-dnspython python3-email-validator python3-h11 python3-httpcore python3-httpx python3-idna python3-linkify-it python3-markdown-it python3-mdurl python3-minimal python3-mpmath python3-numpy python3-numpy-dev python3-optlang python3-pandas python3-pandas-lib python3-platformdirs python3-pydantic python3-pydantic-core python3-pygments python3-pytz python3-rich python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-sniffio python3-swiglpk python3-sympy python3-tabulate python3-typing-extensions python3-uc-micro python3.13 python3.13-minimal readline-common Suggested packages: libiodbc2-dev default-libmysqlclient-dev python3-doc python3-tk python3-venv python3-matplotlib qsopt-ex python3-trio python3-aioquic python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc python3-statsmodels python-pygments-doc ttf-bitstream-vera texlive-fonts-extra dvipng python-sympy-doc python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 python3-cryptography python3-h2 python3-scipy python3-matplotlib python3-tz python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba python3-pil isympy-common The following NEW packages will be installed: ca-certificates libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5 libglpk40 libgomp1 liblapack3 libltdl7 libncursesw6 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsuitesparseconfig7 libxml2 media-types netbase openssl python-cobra-data python3 python3-annotated-types python3-anyio python3-certifi python3-click python3-cobra python3-dateutil python3-depinfo python3-diskcache python3-dnspython python3-email-validator python3-h11 python3-httpcore python3-httpx python3-idna python3-linkify-it python3-markdown-it python3-mdurl python3-minimal python3-mpmath python3-numpy python3-numpy-dev python3-optlang python3-pandas python3-pandas-lib python3-platformdirs python3-pydantic python3-pydantic-core python3-pygments python3-pytz python3-rich python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-sniffio python3-swiglpk python3-sympy python3-tabulate python3-typing-extensions python3-uc-micro python3.13 python3.13-minimal readline-common 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 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Preparing to unpack .../24-python3-depinfo_2.2.0-3_amd64.deb ... Unpacking python3-depinfo (2.2.0-3) ... Selecting previously unselected package python3-diskcache. Preparing to unpack .../25-python3-diskcache_5.6.3-1_all.deb ... Unpacking python3-diskcache (5.6.3-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../26-python3-pygments_2.18.0+dfsg-2_all.deb ... Unpacking python3-pygments (2.18.0+dfsg-2) ... Selecting previously unselected package python3-mdurl. Preparing to unpack .../27-python3-mdurl_0.1.2-1_all.deb ... Unpacking python3-mdurl (0.1.2-1) ... Selecting previously unselected package python3-uc-micro. Preparing to unpack .../28-python3-uc-micro_1.0.3-1_all.deb ... Unpacking python3-uc-micro (1.0.3-1) ... Selecting previously unselected package python3-linkify-it. Preparing to unpack .../29-python3-linkify-it_2.0.3-1_all.deb ... Unpacking python3-linkify-it (2.0.3-1) ... Selecting previously unselected package python3-markdown-it. Preparing to unpack .../30-python3-markdown-it_3.0.0-3_all.deb ... Unpacking python3-markdown-it (3.0.0-3) ... Selecting previously unselected package python3-rich. Preparing to unpack .../31-python3-rich_13.9.4-1_all.deb ... Unpacking python3-rich (13.9.4-1) ... Selecting previously unselected package python3-h11. Preparing to unpack .../32-python3-h11_0.14.0-1.1_all.deb ... Unpacking python3-h11 (0.14.0-1.1) ... Selecting previously unselected package python3-httpcore. Preparing to unpack .../33-python3-httpcore_1.0.7-1_all.deb ... Unpacking python3-httpcore (1.0.7-1) ... Selecting previously unselected package python3-httpx. Preparing to unpack .../34-python3-httpx_0.28.1-1_all.deb ... Unpacking python3-httpx (0.28.1-1) ... Selecting previously unselected package python3-swiglpk. Preparing to unpack .../35-python3-swiglpk_5.0.10-2+b2_amd64.deb ... Unpacking python3-swiglpk (5.0.10-2+b2) ... Selecting previously unselected package python3-mpmath. 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Selecting previously unselected package python3-ruamel.yaml.clib. Preparing to unpack .../48-python3-ruamel.yaml.clib_0.2.12+ds-1+b1_amd64.deb ... Unpacking python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Selecting previously unselected package python3-ruamel.yaml. Preparing to unpack .../49-python3-ruamel.yaml_0.18.10+ds-1_all.deb ... Unpacking python3-ruamel.yaml (0.18.10+ds-1) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../50-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package python3-sbml5. Preparing to unpack .../51-python3-sbml5_5.20.4+dfsg-0.1_amd64.deb ... Unpacking python3-sbml5 (5.20.4+dfsg-0.1) ... Selecting previously unselected package python3-cobra. Preparing to unpack .../52-python3-cobra_0.29.1-3_amd64.deb ... Unpacking python3-cobra (0.29.1-3) ... Setting up media-types (13.0.0) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libblas3:amd64 (3.12.1-6) ... 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 python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libltdl7:amd64 (2.5.4-4) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... Setting up netbase (6.5) ... Setting up openssl (3.5.1-1) ... Setting up python-cobra-data (0.29.1-3) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up liblapack3:amd64 (3.12.1-6) ... 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 libamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up libcolamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libglpk40:amd64 (5.0-1+b2) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libpython3.13:amd64 (3.13.5-2) ... Setting up python3.13 (3.13.5-2) ... Setting up python3 (3.13.5-1) ... Setting up python3-click (8.2.0+0.really.8.1.8-1) ... Setting up python3-annotated-types (0.7.0-1) ... Setting up python3-uc-micro (1.0.3-1) ... Setting up python3-sbml5 (5.20.4+dfsg-0.1) ... Setting up python3-platformdirs (4.3.7-1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up python3-idna (3.10-1) ... Setting up python3-h11 (0.14.0-1.1) ... Setting up python3-depinfo (2.2.0-3) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-dnspython (2.7.0-1) ... Setting up python3-linkify-it (2.0.3-1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-email-validator (2.2.0-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-diskcache (5.6.3-1) ... Setting up python3-swiglpk (5.0.10-2+b2) ... Setting up python3-httpcore (1.0.7-1) ... Setting up python3-sniffio (1.3.1-1) ... Setting up python3-sympy (1.13.3-5) ... Setting up python3-pydantic-core (2.27.2-3+b1) ... Setting up python3-anyio (4.8.0-3) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Setting up python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-pytz (2025.2-3) ... Setting up python3-pandas (2.2.3+dfsg-9) ... Setting up python3-pydantic (2.10.6-2) ... Setting up python3-markdown-it (3.0.0-3) ... Setting up python3-ruamel.yaml (0.18.10+ds-1) ... Setting up python3-optlang (1.8.3-1) ... Setting up python3-rich (13.9.4-1) ... Setting up python3-httpx (0.28.1-1) ... Setting up python3-cobra (0.29.1-3) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-y', 'install', 'python3-cobra'] 0m20.2s INFO: Running scripts post_install 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_install_exceptions'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_install_exceptions'] 0m20.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m20.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m20.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp4_j4uh54 to sid 0m20.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m20.7s INFO: Running scripts pre_distupgrade 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'update'] 0m22.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [216 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7420 kB] Fetched 17.8 MB in 2s (11.7 MB/s) Reading package lists... 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'update'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-yf', 'dist-upgrade'] 0m26.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-15-base The following packages will be upgraded: apt base-files bsdutils gcc-14-base libapt-pkg7.0 libblkid1 libgcc-s1 libgfortran5 libglpk40 libgomp1 liblastlog2-2 libmount1 libpython3.13 libpython3.13-minimal libpython3.13-stdlib libsmartcols1 libssl3t64 libstdc++6 libuuid1 login mount openssl openssl-provider-legacy python3-typing-extensions python3.13 python3.13-minimal tzdata util-linux 28 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After this operation, 780 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 14 [72.9 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41.1-1 [110 kB] Get:3 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41.1-1 [28.6 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41.1-1 [37.7 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41.1-1 [171 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41.1-1 [209 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41.1-1 [143 kB] Get:8 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41.1-1 [1236 kB] Get:9 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41.1-1 [162 kB] Get:10 http://deb.debian.org/debian sid/main amd64 gcc-15-base amd64 15.2.0-1 [52.0 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 15.2.0-1 [71.7 kB] Get:12 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.2-1 [307 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.2-1 [2438 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 15.2.0-1 [736 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.1.4 [1182 kB] Get:16 http://deb.debian.org/debian sid/main amd64 apt amd64 3.1.4 [1478 kB] Get:17 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41.1-1 [115 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.6-1 [761 kB] Get:19 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.6-1 [2218 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpython3.13 amd64 3.13.6-1 [2162 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.6-1 [1959 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.6-1 [864 kB] Get:23 http://deb.debian.org/debian sid/main amd64 tzdata all 2025b-5 [260 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 15.2.0-1 [140 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 15.2.0-1 [862 kB] Get:26 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.3.0-5 [51.5 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libglpk40 amd64 5.0-2 [398 kB] Get:28 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get:29 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.14.1-1 [91.3 kB] Preconfiguring packages ... Fetched 19.8 MB in 0s (70.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13190 files and directories currently installed.) Preparing to unpack .../base-files_14_amd64.deb ... Unpacking base-files (14) over (13.8) ... Setting up base-files (14) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (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 ... 13195 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.5.2-1_amd64.deb ... Unpacking openssl-provider-legacy (3.5.2-1) over (3.5.1-1) ... Setting up openssl-provider-legacy (3.5.2-1) ... (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 ... 13195 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.1.4_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.1.4) over (3.0.3) ... Setting up libapt-pkg7.0:amd64 (3.1.4) ... (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 ... 13193 files and directories currently installed.) Preparing to unpack .../00-login_1%3a4.16.0-2+really2.41.1-1_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.1-1) over (1:4.16.0-2+really2.41-5) ... Preparing to unpack .../01-python3.13_3.13.6-1_amd64.deb ... Unpacking python3.13 (3.13.6-1) over (3.13.5-2) ... Preparing to unpack .../02-python3.13-minimal_3.13.6-1_amd64.deb ... Unpacking python3.13-minimal (3.13.6-1) over (3.13.5-2) ... 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Preparing to unpack .../11-openssl_3.5.2-1_amd64.deb ... Unpacking openssl (3.5.2-1) over (3.5.1-1) ... Preparing to unpack .../12-python3-typing-extensions_4.14.1-1_all.deb ... Unpacking python3-typing-extensions (4.14.1-1) over (4.13.2-1) ... Setting up gcc-14-base:amd64 (14.3.0-5) ... Setting up libgomp1:amd64 (15.2.0-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Aug 12 21:58:12 UTC 2025. Universal Time is now: Tue Aug 12 21:58:12 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.6-1) ... Setting up libglpk40:amd64 (5.0-2) ... Setting up python3-typing-extensions (4.14.1-1) ... Setting up libgfortran5:amd64 (15.2.0-1) ... Setting up mount (2.41.1-1) ... Setting up python3.13-minimal (3.13.6-1) ... Setting up openssl (3.5.2-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.6-1) ... Setting up login (1:4.16.0-2+really2.41.1-1) ... Setting up libpython3.13:amd64 (3.13.6-1) ... Setting up python3.13 (3.13.6-1) ... Processing triggers for libc-bin (2.41-12) ... 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-yf', 'dist-upgrade'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m27.0s DUMP: f068dead4a8770383d92447d1c31799e - 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra'] 0m27.1s DUMP: Package: python3-cobra Source: python-cobra Version: 0.29.1-3 Installed-Size: 1878 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-3), python3-tabulate, python3-sbml5 Suggests: python3-matplotlib, qsopt-ex Description-en: constraint-based modeling of biological networks with Python 3 COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accommodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux balance analysis, flux variability analysis, and gene deletion analyses. Description-md5: 0052f98776eccb61924a15b5d6618e25 Homepage: https://opencobra.github.io/cobrapy/ Section: python Priority: optional Filename: pool/main/p/python-cobra/python3-cobra_0.29.1-3_amd64.deb Size: 1119344 MD5sum: 18e670194f1ec471bc967eb5dc4a3e82 SHA256: 7afc9b545d203492f9017ca53552d392a612d4caa40678646889129b53b5663e 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra'] 0m27.1s INFO: apt-cache knows about the following packages: python3-cobra 0m27.1s INFO: Running scripts pre_install 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_database-server'] 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_database-server'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_exceptions'] 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_exceptions'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_extras'] 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_extras'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy'] 0m27.1s 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: 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy', 'python3-cobra'] 0m27.1s DUMP: python3-cobra: Installed: 0.29.1-3 Candidate: 0.29.1-3 Version table: *** 0.29.1-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy', 'python3-cobra'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-y', 'install', 'python3-cobra'] 0m27.4s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-cobra is already the newest version (0.29.1-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-y', 'install', 'python3-cobra'] 0m27.4s INFO: Running scripts post_install 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_install_exceptions'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_install_exceptions'] 0m27.4s INFO: Running scripts post_distupgrade 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_exceptions'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_exceptions'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_zz_backports'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_distupgrade_zz_backports'] 0m27.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m28.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m28.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m28.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m28.6s INFO: Running scripts pre_install 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_database-server'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_database-server'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_exceptions'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_exceptions'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_extras'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_extras'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy'] 0m28.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy', 'python3-cobra'] 0m28.6s DUMP: python3-cobra: Installed: 0.29.1-3 Candidate: 0.29.1-3 Version table: *** 0.29.1-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-cache', 'policy', 'python3-cobra'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-3'] 0m28.9s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-cobra is already the newest version (0.29.1-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-3'] 0m28.9s INFO: Running scripts post_install 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_install_exceptions'] 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_install_exceptions'] 0m28.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m29.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m29.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', '-ac', '--ignore-obsolete'] 0m30.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', '-ac', '--ignore-obsolete'] 0m30.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.7s DUMP: 0.15.9~deb12u1 0m30.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.7s INFO: Running adequate version 0.15.9~deb12u1 now. 0m30.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'python3-cobra'] 0m30.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'python3-cobra'] 0m30.8s INFO: Running scripts pre_remove 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_exceptions'] 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/pre_remove_exceptions'] 0m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m31.4s DUMP: install ok installed apt apt 3.1.4 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41.1-1 install ok installed ca-certificates ca-certificates 20250419 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-5 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd3:amd64 libamd3 1:7.10.1+dfsg-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.4 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.5-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.5-1 install ok installed libblas3:amd64 libblas3 3.12.1-6 install ok installed libblkid1:amd64 libblkid1 2.41.1-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcolamd3:amd64 libcolamd3 1:7.10.1+dfsg-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libffi8:amd64 libffi8 3.4.8-2 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-1 install ok installed libgfortran5:amd64 libgfortran5 15.2.0-1 install ok installed libglpk40:amd64 libglpk40 5.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgomp1:amd64 libgomp1 15.2.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblapack3:amd64 liblapack3 3.12.1-6 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.1-1 install ok installed libltdl7:amd64 libltdl7 2.5.4-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.1-1 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.5-1 install ok installed libpython3.13:amd64 libpython3.13 3.13.6-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.6-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.6-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.1-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.2-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-1 install ok installed libsuitesparseconfig7:amd64 libsuitesparseconfig7 1:7.10.1+dfsg-1 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41.1-1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-2.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41.1-1 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mount mount 2.41.1-1 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 install ok installed openssl openssl 3.5.2-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.2-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed python-cobra-data python-cobra-data 0.29.1-3 install ok installed python3 python3 3.13.5-1 install ok installed python3-annotated-types python3-annotated-types 0.7.0-1 install ok installed python3-anyio python3-anyio 4.8.0-3 install ok installed python3-certifi python3-certifi 2025.1.31+ds-1 install ok installed python3-click python3-click 8.2.0+0.really.8.1.8-1 install ok installed python3-cobra python3-cobra 0.29.1-3 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-depinfo python3-depinfo 2.2.0-3 install ok installed python3-diskcache python3-diskcache 5.6.3-1 install ok installed python3-dnspython python3-dnspython 2.7.0-1 install ok installed python3-email-validator python3-email-validator 2.2.0-1 install ok installed python3-h11 python3-h11 0.14.0-1.1 install ok installed python3-httpcore python3-httpcore 1.0.7-1 install ok installed python3-httpx python3-httpx 0.28.1-1 install ok installed python3-idna python3-idna 3.10-1 install ok installed python3-linkify-it python3-linkify-it 2.0.3-1 install ok installed python3-markdown-it python3-markdown-it 3.0.0-3 install ok installed python3-mdurl python3-mdurl 0.1.2-1 install ok installed python3-minimal python3-minimal 3.13.5-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1 install ok installed python3-optlang python3-optlang 1.8.3-1 install ok installed python3-pandas python3-pandas 2.2.3+dfsg-9 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-9 install ok installed python3-platformdirs python3-platformdirs 4.3.7-1 install ok installed python3-pydantic python3-pydantic 2.10.6-2 install ok installed python3-pydantic-core python3-pydantic-core 2.27.2-3+b1 install ok installed python3-pygments python3-pygments 2.18.0+dfsg-2 install ok installed python3-pytz python3-pytz 2025.2-3 install ok installed python3-rich python3-rich 13.9.4-1 install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.18.10+ds-1 install ok installed python3-ruamel.yaml.clib python3-ruamel.yaml.clib 0.2.12+ds-1+b1 install ok installed python3-sbml5 python3-sbml5 5.20.4+dfsg-0.1 install ok installed python3-sniffio python3-sniffio 1.3.1-1 install ok installed python3-swiglpk python3-swiglpk 5.0.10-2+b2 install ok installed python3-sympy python3-sympy 1.13.3-5 install ok installed python3-tabulate python3-tabulate 0.9.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.14.1-1 install ok installed python3-uc-micro python3-uc-micro 1.0.3-1 install ok installed python3.13 python3.13 3.13.6-1 install ok installed python3.13-minimal python3.13-minimal 3.13.6-1 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.1-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsuitesparseconfig7:amd64', 'libxml2:amd64', 'media-types', 'netbase', 'openssl', 'python-cobra-data', 'python3', 'python3-annotated-types', 'python3-anyio', 'python3-certifi', 'python3-click', 'python3-dateutil', 'python3-depinfo', 'python3-diskcache', 'python3-dnspython', 'python3-email-validator', 'python3-h11', 'python3-httpcore', 'python3-httpx', 'python3-idna', 'python3-linkify-it', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-cobra'] 0m34.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5 libglpk40 libgomp1 liblapack3 libltdl7 libncursesw6 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsuitesparseconfig7 libxml2 media-types netbase openssl python-cobra-data python3 python3-annotated-types python3-anyio python3-certifi python3-click python3-cobra python3-dateutil python3-depinfo python3-diskcache python3-dnspython python3-email-validator python3-h11 python3-httpcore python3-httpx python3-idna python3-linkify-it python3-markdown-it python3-mdurl python3-minimal python3-mpmath python3-numpy python3-numpy-dev python3-optlang python3-pandas python3-pandas-lib python3-platformdirs python3-pydantic python3-pydantic-core python3-pygments python3-pytz python3-rich python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-sniffio python3-swiglpk python3-sympy python3-tabulate python3-typing-extensions python3-uc-micro python3.13 python3.13-minimal readline-common 0 upgraded, 0 newly installed, 66 to remove and 0 not upgraded. After this operation, 236 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 ... 13194 files and directories currently installed.) Removing python3-cobra (0.29.1-3) ... Removing python3-httpx (0.28.1-1) ... Removing python3-httpcore (1.0.7-1) ... Removing python3-certifi (2025.1.31+ds-1) ... Removing ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-optlang (1.8.3-1) ... Removing python3-swiglpk (5.0.10-2+b2) ... Removing libglpk40:amd64 (5.0-2) ... Removing libamd3:amd64 (1:7.10.1+dfsg-1) ... Removing python3-pandas (2.2.3+dfsg-9) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing liblapack3:amd64 (3.12.1-6) ... Removing libblas3:amd64 (3.12.1-6) ... Removing libcolamd3:amd64 (1:7.10.1+dfsg-1) ... Removing python3-ruamel.yaml (0.18.10+ds-1) ... Removing python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Removing python3-rich (13.9.4-1) ... Removing python3-markdown-it (3.0.0-3) ... Removing python3-linkify-it (2.0.3-1) ... Removing python3-uc-micro (1.0.3-1) ... Removing python3-anyio (4.8.0-3) ... Removing python3-pydantic (2.10.6-2) ... Removing python3-pydantic-core (2.27.2-3+b1) ... Removing python3-sympy (1.13.3-5) ... Removing python3-annotated-types (0.7.0-1) ... Removing python3-sbml5 (5.20.4+dfsg-0.1) ... Removing libpython3.13:amd64 (3.13.6-1) ... Removing libgfortran5:amd64 (15.2.0-1) ... Removing libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... Removing libgomp1:amd64 (15.2.0-1) ... Removing libltdl7:amd64 (2.5.4-4) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Removing python3-email-validator (2.2.0-1) ... Removing python3-dnspython (2.7.0-1) ... Removing openssl (3.5.2-1) ... Removing python-cobra-data (0.29.1-3) ... Removing python3-click (8.2.0+0.really.8.1.8-1) ... Removing python3-dateutil (2.9.0-4) ... Removing python3-depinfo (2.2.0-3) ... Removing python3-diskcache (5.6.3-1) ... Removing python3-h11 (0.14.0-1.1) ... Removing python3-idna (3.10-1) ... Removing python3-mdurl (0.1.2-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing python3-platformdirs (4.3.7-1) ... Removing python3-pygments (2.18.0+dfsg-2) ... Removing python3-pytz (2025.2-3) ... Removing python3-sniffio (1.3.1-1) ... Removing python3-tabulate (0.9.0-1) ... Removing python3-typing-extensions (4.14.1-1) ... Removing python3 (3.13.5-1) ... Removing python3.13 (3.13.6-1) ... Removing python3-minimal (3.13.5-1) ... Removing python3.13-minimal (3.13.6-1) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libpython3-stdlib:amd64 (3.13.5-1) ... Removing libpython3.13-stdlib:amd64 (3.13.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.8-2) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libpython3.13-minimal:amd64 (3.13.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing media-types (13.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.41-12) ... 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsuitesparseconfig7:amd64', 'libxml2:amd64', 'media-types', 'netbase', 'openssl', 'python-cobra-data', 'python3', 'python3-annotated-types', 'python3-anyio', 'python3-certifi', 'python3-click', 'python3-dateutil', 'python3-depinfo', 'python3-diskcache', 'python3-dnspython', 'python3-email-validator', 'python3-h11', 'python3-httpcore', 'python3-httpx', 'python3-idna', 'python3-linkify-it', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-cobra'] 0m34.0s INFO: Running scripts post_remove 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_remove_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_remove_exceptions'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--purge', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsuitesparseconfig7:amd64', 'libxml2:amd64', 'media-types', 'netbase', 'openssl', 'python-cobra-data', 'python3', 'python3-annotated-types', 'python3-anyio', 'python3-certifi', 'python3-click', 'python3-dateutil', 'python3-depinfo', 'python3-diskcache', 'python3-dnspython', 'python3-email-validator', 'python3-h11', 'python3-httpcore', 'python3-httpx', 'python3-idna', 'python3-linkify-it', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m34.0s DUMP: (Reading database ... 4952 files and directories currently installed.) Purging configuration files for ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove libamd3 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libcolamd3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libglpk40 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libltdl7 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.13 which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.6-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libsuitesparseconfig7 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed Purging configuration files for media-types (13.0.0) ... Purging configuration files for netbase (6.5) ... Purging configuration files for openssl (3.5.2-1) ... dpkg: warning: ignoring request to remove python-cobra-data which isn't installed Purging configuration files for python3 (3.13.5-1) ... dpkg: warning: ignoring request to remove python3-annotated-types which isn't installed dpkg: warning: ignoring request to remove python3-anyio which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-click which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-depinfo which isn't installed dpkg: warning: ignoring request to remove python3-diskcache which isn't installed dpkg: warning: ignoring request to remove python3-dnspython which isn't installed dpkg: warning: ignoring request to remove python3-email-validator which isn't installed dpkg: warning: ignoring request to remove python3-h11 which isn't installed dpkg: warning: ignoring request to remove python3-httpcore which isn't installed dpkg: warning: ignoring request to remove python3-httpx which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-linkify-it which isn't installed dpkg: warning: ignoring request to remove python3-markdown-it which isn't installed dpkg: warning: ignoring request to remove python3-mdurl which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed Purging configuration files for python3-numpy (1:2.2.4+ds-1) ... dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-optlang which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-pydantic which isn't installed dpkg: warning: ignoring request to remove python3-pydantic-core which isn't installed dpkg: warning: ignoring request to remove python3-pygments which isn't installed dpkg: warning: ignoring request to remove python3-pytz which isn't installed dpkg: warning: ignoring request to remove python3-rich which isn't installed dpkg: warning: ignoring request to remove python3-ruamel.yaml which isn't installed dpkg: warning: ignoring request to remove python3-ruamel.yaml.clib which isn't installed dpkg: warning: ignoring request to remove python3-sbml5 which isn't installed dpkg: warning: ignoring request to remove python3-sniffio which isn't installed dpkg: warning: ignoring request to remove python3-swiglpk which isn't installed Purging configuration files for python3-sympy (1.13.3-5) ... dpkg: warning: ignoring request to remove python3-tabulate which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-uc-micro which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.6-1) ... Purging configuration files for readline-common (8.2-6) ... 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--purge', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libltdl7:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsuitesparseconfig7:amd64', 'libxml2:amd64', 'media-types', 'netbase', 'openssl', 'python-cobra-data', 'python3', 'python3-annotated-types', 'python3-anyio', 'python3-certifi', 'python3-click', 'python3-dateutil', 'python3-depinfo', 'python3-diskcache', 'python3-dnspython', 'python3-email-validator', 'python3-h11', 'python3-httpcore', 'python3-httpx', 'python3-idna', 'python3-linkify-it', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--purge', 'python3-cobra'] 0m34.0s DUMP: dpkg: warning: ignoring request to remove python3-cobra which isn't installed 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--purge', 'python3-cobra'] 0m34.0s INFO: Running scripts post_purge 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_purge_exceptions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_purge_exceptions'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--purge', '--pending'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--purge', '--pending'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--remove', '--pending'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg', '--remove', '--pending'] 0m34.1s INFO: Running scripts post_test 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_test_exceptions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'tmp/scripts/post_test_exceptions'] 0m34.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m34.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg-divert', '--list'] 0m34.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 /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 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'dpkg-divert', '--list'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'clean'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54', 'apt-get', 'clean'] 0m34.3s DEBUG: Recording chroot state 0m34.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/shm'] 0m34.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/shm'] 0m34.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/console'] 0m34.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/console'] 0m34.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/ptmx'] 0m34.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/ptmx'] 0m34.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/pts'] 0m34.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/dev/pts'] 0m34.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/proc'] 0m35.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54/proc'] 0m35.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m35.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp4_j4uh54'] 0m35.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp4_j4uh54 0m35.0s INFO: PASS: Upgrading between Debian distributions. 0m35.0s INFO: PASS: All tests. 0m35.0s INFO: piuparts run ends. ret=0 End: 2025-08-12 21:58:22 GMT