Start: 2026-02-28 04:31:37 GMT Package: python3-cobra Source: python-cobra Version: 0.29.1-4 Installed-Size: 1876 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python-cobra-data (= 0.29.1-4), python3-numpy, python3-pandas, python3-ruamel.yaml, python3-sbml5, python3-swiglpk (>= 5.0.8-1~), python3-tabulate, python3-depinfo, python3-diskcache, python3-httpx, python3-optlang (>= 1.7.0-1~), python3-platformdirs, python3-pydantic, python3-rich, python3:any 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_0.29.1-4_amd64.deb Size: 1118236 MD5sum: 869c747f56f90d091557112d30b8745b SHA256: a2794d871a590990b4e75a0eedfe7e2c9cc422940a9fd78c610765555b604c84 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt python3-cobra=0.29.1-4 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 1.6.1~202508211944~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt python3-cobra=0.29.1-4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-43-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.162-1 (2026-02-08) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpvfg66lca 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpvfg66lca 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/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/tmpvfg66lca/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/tmpvfg66lca/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid 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-log-alternatives to /srv/piuparts.debian.org/tmp/tmpvfg66lca/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpvfg66lca/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', 'update'] 0m3.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [187 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.3 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7492 kB] Fetched 17.9 MB in 2s (8410 kB/s) Reading package lists... 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', 'update'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s DUMP: 33c7e74460b374c64edf181f36fe234c - 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s INFO: Running scripts post_setup 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '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/tmpvfg66lca', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s 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' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', 'clean'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', 'clean'] 0m4.9s DEBUG: Recording chroot state 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.2s DUMP: install ok installed apt apt 3.1.16 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-2 install ok installed bsdutils bsdutils 1:2.41.3-4 install ok installed coreutils coreutils 9.10-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.5 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-14 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-3 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.16 install ok installed libattr1:amd64 libattr1 1:2.5.2-4 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b1 install ok installed libblkid1:amd64 libblkid1 2.41.3-4 install ok installed libbsd0:amd64 libbsd0 0.12.2-2+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b1 install ok installed libc-bin libc-bin 2.42-13 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.42-13 install ok installed libc6:amd64 libc6 2.42-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.282+b2 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-14 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-8 install ok installed liblzma5:amd64 liblzma5 5.8.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b2 install ok installed libmount1:amd64 libmount1 2.41.3-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5+b1 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1+b1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2+b1 install ok installed libselinux1:amd64 libselinux1 3.9-4+b1 install ok installed libsemanage-common libsemanage-common 3.9-1 install ok installed libsemanage2:amd64 libsemanage2 3.9-1+b1 install ok installed libsepol2:amd64 libsepol2 3.9-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.3-4 install ok installed libssl3t64:amd64 libssl3t64 3.5.5-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 260~rc1-2 install ok installed libtinfo6:amd64 libtinfo6 6.6+20251231-1 install ok installed libudev1:amd64 libudev1 260~rc1-2 install ok installed libuuid1:amd64 libuuid1 2.41.3-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-3+b1 install ok installed login login 1:4.16.0-2+really2.41.3-4 install ok installed login.defs login.defs 1:4.19.3-1 install ok installed mawk mawk 1.3.4.20260129-1 install ok installed mount mount 2.41.3-4 install ok installed ncurses-base ncurses-base 6.6+20251231-1 install ok installed ncurses-bin ncurses-bin 6.6+20251231-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.5-1 install ok installed passwd passwd 1:4.19.3-1 install ok installed perl-base perl-base 5.40.1-7 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-5 install ok installed sysvinit-utils sysvinit-utils 3.15-6 install ok installed tar tar 1.35+dfsg-4 install ok installed tzdata tzdata 2025c-3 install ok installed util-linux util-linux 2.41.3-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-3 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-divert', '--list'] 0m5.2s 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 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-divert', '--list'] 0m5.2s INFO: Running scripts is_testable 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s INFO: apt-cache does not know about any of the requested packages 0m5.2s INFO: Running scripts pre_test 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_test_root_password'] 0m5.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_test_root_password'] 0m5.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m5.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m5.8s DEBUG: No broken symlinks as far as we can find. 0m5.8s INFO: Running scripts pre_install 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_log_alternatives'] 0m5.9s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_install_log_alternatives'] 0m5.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m6.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m6.4s DEBUG: No broken symlinks as far as we can find. 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-cache', 'policy'] 0m7.1s 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: 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-cache', 'policy'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-cache', 'policy', 'python3-cobra'] 0m7.1s DUMP: python3-cobra: Installed: (none) Candidate: 0.29.1-4 Version table: 0.29.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-cache', 'policy', 'python3-cobra'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-4'] 0m32.6s DUMP: Reading package lists... Building dependency tree... Solving dependencies... 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 libsqlite3-0 libsuitesparseconfig7 libxml2-16 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-swiglpk python3-sympy python3-tabulate python3-typing-extensions python3-typing-inspection 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-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 libsqlite3-0 libsuitesparseconfig7 libxml2-16 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-swiglpk python3-sympy python3-tabulate python3-typing-extensions python3-typing-inspection python3-uc-micro python3.13 python3.13-minimal readline-common 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 55.0 MB of archives. After this operation, 277 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Get:3 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Get:5 http://deb.debian.org/debian sid/main amd64 media-types all 14.0.0 [30.8 kB] Get:6 http://deb.debian.org/debian sid/main amd64 netbase all 6.5 [12.4 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.3-4 [74.8 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-9 [920 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Get:13 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [138 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-7+b1 [209 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 15.2.0-14 [862 kB] Get:19 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-7+b1 [2550 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [7487 kB] Get:21 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.5-1 [1500 kB] Get:22 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20260223 [158 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 15.2.0-14 [140 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libsuitesparseconfig7 amd64 1:7.12.2+dfsg-1 [33.7 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libamd3 amd64 1:7.12.2+dfsg-1 [50.6 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libcolamd3 amd64 1:7.12.2+dfsg-1 [42.5 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libltdl7 amd64 2.5.4-9 [416 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libglpk40 amd64 5.0-2+b1 [392 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libpython3.13 amd64 3.13.12-1 [2187 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:31 http://deb.debian.org/debian sid/main amd64 python-cobra-data all 0.29.1-4 [1437 kB] Get:32 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.15.0-2 [92.5 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-annotated-types all 0.7.0-1 [18.8 kB] Get:34 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.11-1 [41.7 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-anyio all 4.12.1-1 [75.1 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2026.2.25+ds-1 [9612 B] Get:37 http://deb.debian.org/debian sid/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB] Get:38 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get:39 http://deb.debian.org/debian sid/main amd64 python3-pytz all 2025.2-5 [31.8 kB] Get:40 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6583 kB] Get:41 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.3.3+dfsg-3 [2935 kB] Get:42 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.15+ds-1 [181 kB] Get:43 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get:44 http://deb.debian.org/debian sid/main amd64 python3-sbml5 amd64 5.20.5+dfsg-3 [3534 kB] Get:45 http://deb.debian.org/debian sid/main amd64 python3-swiglpk amd64 5.0.10-2+b3 [92.5 kB] Get:46 http://deb.debian.org/debian sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get:47 http://deb.debian.org/debian sid/main amd64 python3-depinfo amd64 2.2.0-4 [11.7 kB] Get:48 http://deb.debian.org/debian sid/main amd64 python3-diskcache all 5.6.3-1 [34.4 kB] Get:49 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.19.2+dfsg-1 [847 kB] Get:50 http://deb.debian.org/debian sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get:51 http://deb.debian.org/debian sid/main amd64 python3-uc-micro all 1.0.3-1 [5744 B] Get:52 http://deb.debian.org/debian sid/main amd64 python3-linkify-it all 2.0.3-2 [18.6 kB] Get:53 http://deb.debian.org/debian sid/main amd64 python3-markdown-it all 3.0.0-3 [59.5 kB] Get:54 http://deb.debian.org/debian sid/main amd64 python3-rich all 13.9.4-1.2 [203 kB] Get:55 http://deb.debian.org/debian sid/main amd64 python3-h11 all 0.14.0-1.1 [50.6 kB] Get:56 http://deb.debian.org/debian sid/main amd64 python3-httpcore all 1.0.9-1 [45.0 kB] Get:57 http://deb.debian.org/debian sid/main amd64 python3-httpx all 0.28.1-1 [76.2 kB] Get:58 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.4.0-1 [448 kB] Get:59 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get:60 http://deb.debian.org/debian sid/main amd64 python3-optlang all 1.8.3-1 [5375 kB] Get:61 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.9.2-1 [18.4 kB] Get:62 http://deb.debian.org/debian sid/main amd64 python3-pydantic-core amd64 2.41.5-2+b1 [2193 kB] Get:63 http://deb.debian.org/debian sid/main amd64 python3-typing-inspection all 0.4.2-1 [13.8 kB] Get:64 http://deb.debian.org/debian sid/main amd64 python3-dnspython all 2.7.0-1 [164 kB] Get:65 http://deb.debian.org/debian sid/main amd64 python3-email-validator all 2.2.0-1 [31.6 kB] Get:66 http://deb.debian.org/debian sid/main amd64 python3-pydantic amd64 2.12.5-2 [380 kB] Get:67 http://deb.debian.org/debian sid/main amd64 python3-cobra amd64 0.29.1-4 [1118 kB] Preconfiguring packages ... Fetched 55.0 MB in 0s (135 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4905 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.4-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.12-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.12-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.12-1_amd64.deb ... Unpacking python3.13-minimal (3.13.12-1) ... Setting up libpython3.13-minimal:amd64 (3.13.12-1) ... Setting up libexpat1:amd64 (2.7.4-1) ... Setting up python3.13-minimal (3.13.12-1) ... 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 ... 5239 files and directories currently installed.) 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.46.1-9_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-9) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../08-libpython3.13-stdlib_3.13.12-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.12-1) ... 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Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../26-python3-pandas_2.3.3+dfsg-3_all.deb ... Unpacking python3-pandas (2.3.3+dfsg-3) ... Selecting previously unselected package python3-ruamel.yaml.clib. Preparing to unpack .../27-python3-ruamel.yaml.clib_0.2.15+ds-1_amd64.deb ... Unpacking python3-ruamel.yaml.clib (0.2.15+ds-1) ... Selecting previously unselected package python3-ruamel.yaml. Preparing to unpack .../28-python3-ruamel.yaml_0.18.10+ds-1_all.deb ... Unpacking python3-ruamel.yaml (0.18.10+ds-1) ... Selecting previously unselected package python3-sbml5. Preparing to unpack .../29-python3-sbml5_5.20.5+dfsg-3_amd64.deb ... Unpacking python3-sbml5 (5.20.5+dfsg-3) ... Selecting previously unselected package python3-swiglpk. Preparing to unpack .../30-python3-swiglpk_5.0.10-2+b3_amd64.deb ... Unpacking python3-swiglpk (5.0.10-2+b3) ... Selecting previously unselected package python3-tabulate. 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Preparing to unpack .../37-python3-linkify-it_2.0.3-2_all.deb ... Unpacking python3-linkify-it (2.0.3-2) ... Selecting previously unselected package python3-markdown-it. Preparing to unpack .../38-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 .../39-python3-rich_13.9.4-1.2_all.deb ... Unpacking python3-rich (13.9.4-1.2) ... Selecting previously unselected package python3-h11. Preparing to unpack .../40-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 .../41-python3-httpcore_1.0.9-1_all.deb ... Unpacking python3-httpcore (1.0.9-1) ... Selecting previously unselected package python3-httpx. Preparing to unpack .../42-python3-httpx_0.28.1-1_all.deb ... Unpacking python3-httpx (0.28.1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../43-python3-mpmath_1.4.0-1_all.deb ... Unpacking python3-mpmath (1.4.0-1) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../44-python3-sympy_1.14.0-2_all.deb ... Unpacking python3-sympy (1.14.0-2) ... Selecting previously unselected package python3-optlang. Preparing to unpack .../45-python3-optlang_1.8.3-1_all.deb ... Unpacking python3-optlang (1.8.3-1) ... Selecting previously unselected package python3-platformdirs. Preparing to unpack .../46-python3-platformdirs_4.9.2-1_all.deb ... Unpacking python3-platformdirs (4.9.2-1) ... Selecting previously unselected package python3-pydantic-core. Preparing to unpack .../47-python3-pydantic-core_2.41.5-2+b1_amd64.deb ... Unpacking python3-pydantic-core (2.41.5-2+b1) ... Selecting previously unselected package python3-typing-inspection. Preparing to unpack .../48-python3-typing-inspection_0.4.2-1_all.deb ... Unpacking python3-typing-inspection (0.4.2-1) ... Selecting previously unselected package python3-dnspython. Preparing to unpack .../49-python3-dnspython_2.7.0-1_all.deb ... Unpacking python3-dnspython (2.7.0-1) ... Selecting previously unselected package python3-email-validator. Preparing to unpack .../50-python3-email-validator_2.2.0-1_all.deb ... Unpacking python3-email-validator (2.2.0-1) ... Selecting previously unselected package python3-pydantic. Preparing to unpack .../51-python3-pydantic_2.12.5-2_amd64.deb ... Unpacking python3-pydantic (2.12.5-2) ... Selecting previously unselected package python3-cobra. Preparing to unpack .../52-python3-cobra_0.29.1-4_amd64.deb ... Unpacking python3-cobra (0.29.1-4) ... Setting up media-types (14.0.0) ... Setting up libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Setting up libsqlite3-0:amd64 (3.46.1-9) ... Setting up libgomp1:amd64 (15.2.0-14) ... Setting up libblas3:amd64 (3.12.1-7+b1) ... 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 (1:2.3.5+ds-3) ... Setting up libncursesw6:amd64 (6.6+20251231-1) ... Setting up libltdl7:amd64 (2.5.4-9) ... Setting up libgfortran5:amd64 (15.2.0-14) ... Setting up libffi8:amd64 (3.5.2-3+b1) ... Setting up libsuitesparseconfig7:amd64 (1:7.12.2+dfsg-1) ... Setting up netbase (6.5) ... Setting up openssl (3.5.5-1) ... Setting up python-cobra-data (0.29.1-4) ... Setting up readline-common (8.3-4) ... Setting up liblapack3:amd64 (3.12.1-7+b1) ... 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 (1:7.12.2+dfsg-1) ... Setting up libcolamd3:amd64 (1:7.12.2+dfsg-1) ... Setting up ca-certificates (20260223) ... Updating certificates in /etc/ssl/certs... 144 added, 0 removed; done. Setting up libglpk40:amd64 (5.0-2+b1) ... Setting up libreadline8t64:amd64 (8.3-4) ... Setting up libpython3.13-stdlib:amd64 (3.13.12-1) ... Setting up libpython3-stdlib:amd64 (3.13.9-3) ... Setting up libpython3.13:amd64 (3.13.12-1) ... Setting up python3.13 (3.13.12-1) ... Setting up python3 (3.13.9-3) ... 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 (5.20.5+dfsg-3) ... Setting up python3-platformdirs (4.9.2-1) ... Setting up python3-pygments (2.19.2+dfsg-1) ... Setting up python3-certifi (2026.2.25+ds-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up python3-idna (3.11-1) ... Setting up python3-h11 (0.14.0-1.1) ... Setting up python3-depinfo (2.2.0-4) ... Setting up python3-typing-extensions (4.15.0-2) ... Setting up python3-numpy (1:2.3.5+ds-3) ... Setting up python3-dnspython (2.7.0-1) ... Setting up python3-linkify-it (2.0.3-2) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-email-validator (2.2.0-1) ... Setting up python3-mpmath (1.4.0-1) ... Setting up python3-diskcache (5.6.3-1) ... Setting up python3-swiglpk (5.0.10-2+b3) ... Setting up python3-httpcore (1.0.9-1) ... Setting up python3-sympy (1.14.0-2) ... Setting up python3-pydantic-core (2.41.5-2+b1) ... Setting up python3-typing-inspection (0.4.2-1) ... Setting up python3-anyio (4.12.1-1) ... Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... Setting up python3-ruamel.yaml.clib (0.2.15+ds-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-pytz (2025.2-5) ... Setting up python3-pandas (2.3.3+dfsg-3) ... Setting up python3-pydantic (2.12.5-2) ... 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 (13.9.4-1.2) ... Setting up python3-httpx (0.28.1-1) ... Setting up python3-cobra (0.29.1-4) ... Processing triggers for libc-bin (2.42-13) ... Processing triggers for ca-certificates (20260223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-4'] 0m32.6s INFO: Running scripts post_install 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_install_exceptions'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_install_exceptions'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_install_log_alternatives'] 0m32.6s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=python3-cobra=0.29.1-4: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=python3-cobra=0.29.1-4: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=python3-cobra=0.29.1-4: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_install_log_alternatives'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'systemd-tmpfiles', '--cat-config'] 0m32.6s DUMP: chroot: failed to run command 'systemd-tmpfiles': No such file or directory 0m32.6s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'systemd-tmpfiles', '--cat-config'] 0m32.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m33.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m34.6s DEBUG: No broken symlinks as far as we can find. 0m35.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '-ac', '--ignore-obsolete'] 0m36.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '-ac', '--ignore-obsolete'] 0m36.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m36.5s DUMP: 0.15.9~deb12u1 0m36.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m36.5s INFO: Running adequate version 0.15.9~deb12u1 now. 0m36.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'python3-cobra'] 0m36.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'python3-cobra'] 0m36.6s INFO: Running scripts pre_remove 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_exceptions'] 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/pre_remove_exceptions'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.4s DUMP: install ok installed apt apt 3.1.16 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-2 install ok installed bsdutils bsdutils 1:2.41.3-4 install ok installed ca-certificates ca-certificates 20260223 install ok installed coreutils coreutils 9.10-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.5 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-14 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-3 install ok installed libamd3:amd64 libamd3 1:7.12.2+dfsg-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.16 install ok installed libattr1:amd64 libattr1 1:2.5.2-4 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b1 install ok installed libblas3:amd64 libblas3 3.12.1-7+b1 install ok installed libblkid1:amd64 libblkid1 2.41.3-4 install ok installed libbsd0:amd64 libbsd0 0.12.2-2+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b1 install ok installed libc-bin libc-bin 2.42-13 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.42-13 install ok installed libc6:amd64 libc6 2.42-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.1-1 install ok installed libcolamd3:amd64 libcolamd3 1:7.12.2+dfsg-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.282+b2 install ok installed libexpat1:amd64 libexpat1 2.7.4-1 install ok installed libffi8:amd64 libffi8 3.5.2-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-14 install ok installed libgfortran5:amd64 libgfortran5 15.2.0-14 install ok installed libglpk40:amd64 libglpk40 5.0-2+b1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b1 install ok installed libgomp1:amd64 libgomp1 15.2.0-14 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblapack3:amd64 liblapack3 3.12.1-7+b1 install ok installed libltdl7:amd64 libltdl7 2.5.4-9 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-8 install ok installed liblzma5:amd64 liblzma5 5.8.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b2 install ok installed libmount1:amd64 libmount1 2.41.3-4 install ok installed libncursesw6:amd64 libncursesw6 6.6+20251231-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5+b1 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.9-3 install ok installed libpython3.13:amd64 libpython3.13 3.13.12-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.12-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.12-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.3-4 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2+b1 install ok installed libselinux1:amd64 libselinux1 3.9-4+b1 install ok installed libsemanage-common libsemanage-common 3.9-1 install ok installed libsemanage2:amd64 libsemanage2 3.9-1+b1 install ok installed libsepol2:amd64 libsepol2 3.9-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.3-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-9 install ok installed libssl3t64:amd64 libssl3t64 3.5.5-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-14 install ok installed libsuitesparseconfig7:amd64 libsuitesparseconfig7 1:7.12.2+dfsg-1 install ok installed libsystemd0:amd64 libsystemd0 260~rc1-2 install ok installed libtinfo6:amd64 libtinfo6 6.6+20251231-1 install ok installed libudev1:amd64 libudev1 260~rc1-2 install ok installed libuuid1:amd64 libuuid1 2.41.3-4 install ok installed libxml2-16:amd64 libxml2-16 2.15.1+dfsg-2+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-3+b1 install ok installed login login 1:4.16.0-2+really2.41.3-4 install ok installed login.defs login.defs 1:4.19.3-1 install ok installed mawk mawk 1.3.4.20260129-1 install ok installed media-types media-types 14.0.0 install ok installed mount mount 2.41.3-4 install ok installed ncurses-base ncurses-base 6.6+20251231-1 install ok installed ncurses-bin ncurses-bin 6.6+20251231-1 install ok installed netbase netbase 6.5 install ok installed openssl openssl 3.5.5-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.5-1 install ok installed passwd passwd 1:4.19.3-1 install ok installed perl-base perl-base 5.40.1-7 install ok installed python-cobra-data python-cobra-data 0.29.1-4 install ok installed python3 python3 3.13.9-3 install ok installed python3-annotated-types python3-annotated-types 0.7.0-1 install ok installed python3-anyio python3-anyio 4.12.1-1 install ok installed python3-certifi python3-certifi 2026.2.25+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 0.29.1-4 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-depinfo python3-depinfo 2.2.0-4 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 1.0.9-1 install ok installed python3-httpx python3-httpx 0.28.1-1 install ok installed python3-idna python3-idna 3.11-1 install ok installed python3-linkify-it python3-linkify-it 2.0.3-2 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 3.13.9-3 install ok installed python3-mpmath python3-mpmath 1.4.0-1 install ok installed python3-numpy python3-numpy 1:2.3.5+ds-3 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.3.5+ds-3 install ok installed python3-optlang python3-optlang 1.8.3-1 install ok installed python3-pandas python3-pandas 2.3.3+dfsg-3 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.3.3+dfsg-3 install ok installed python3-platformdirs python3-platformdirs 4.9.2-1 install ok installed python3-pydantic python3-pydantic 2.12.5-2 install ok installed python3-pydantic-core python3-pydantic-core 2.41.5-2+b1 install ok installed python3-pygments python3-pygments 2.19.2+dfsg-1 install ok installed python3-pytz python3-pytz 2025.2-5 install ok installed python3-rich python3-rich 13.9.4-1.2 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 0.2.15+ds-1 install ok installed python3-sbml5 python3-sbml5 5.20.5+dfsg-3 install ok installed python3-swiglpk python3-swiglpk 5.0.10-2+b3 install ok installed python3-sympy python3-sympy 1.14.0-2 install ok installed python3-tabulate python3-tabulate 0.9.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.15.0-2 install ok installed python3-typing-inspection python3-typing-inspection 0.4.2-1 install ok installed python3-uc-micro python3-uc-micro 1.0.3-1 install ok installed python3.13 python3.13 3.13.12-1 install ok installed python3.13-minimal python3.13-minimal 3.13.12-1 install ok installed readline-common readline-common 8.3-4 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-5 install ok installed sysvinit-utils sysvinit-utils 3.15-6 install ok installed tar tar 1.35+dfsg-4 install ok installed tzdata tzdata 2025c-3 install ok installed util-linux util-linux 2.41.3-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-3 0m37.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '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', 'libsqlite3-0:amd64', 'libsuitesparseconfig7:amd64', 'libxml2-16: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-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-typing-inspection', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-cobra'] 0m42.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... 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 libsqlite3-0 libsuitesparseconfig7 libxml2-16 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-swiglpk python3-sympy python3-tabulate python3-typing-extensions python3-typing-inspection python3-uc-micro python3.13 python3.13-minimal readline-common 0 upgraded, 0 newly installed, 67 to remove and 0 not upgraded. After this operation, 277 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 ... 12707 files and directories currently installed.) Removing python3-cobra (0.29.1-4) ... Removing python3-httpx (0.28.1-1) ... Removing python3-httpcore (1.0.9-1) ... Removing python3-certifi (2026.2.25+ds-1) ... Removing ca-certificates (20260223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-optlang (1.8.3-1) ... Removing python3-swiglpk (5.0.10-2+b3) ... Removing libglpk40:amd64 (5.0-2+b1) ... Removing libamd3:amd64 (1:7.12.2+dfsg-1) ... Removing python3-pandas (2.3.3+dfsg-3) ... Removing python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... Removing python3-numpy (1:2.3.5+ds-3) ... Removing liblapack3:amd64 (3.12.1-7+b1) ... Removing libblas3:amd64 (3.12.1-7+b1) ... Removing libcolamd3:amd64 (1:7.12.2+dfsg-1) ... Removing python3-ruamel.yaml (0.18.10+ds-1) ... Removing python3-ruamel.yaml.clib (0.2.15+ds-1) ... Removing python3-rich (13.9.4-1.2) ... Removing python3-markdown-it (3.0.0-3) ... Removing python3-linkify-it (2.0.3-2) ... Removing python3-uc-micro (1.0.3-1) ... Removing python3-anyio (4.12.1-1) ... Removing python3-pydantic (2.12.5-2) ... Removing python3-pydantic-core (2.41.5-2+b1) ... Removing python3-sympy (1.14.0-2) ... Removing python3-annotated-types (0.7.0-1) ... Removing python3-sbml5 (5.20.5+dfsg-3) ... Removing libpython3.13:amd64 (3.13.12-1) ... Removing libgfortran5:amd64 (15.2.0-14) ... Removing libsuitesparseconfig7:amd64 (1:7.12.2+dfsg-1) ... Removing libgomp1:amd64 (15.2.0-14) ... Removing libltdl7:amd64 (2.5.4-9) ... Removing libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Removing python3-email-validator (2.2.0-1) ... Removing python3-dnspython (2.7.0-1) ... Removing openssl (3.5.5-1) ... Removing python-cobra-data (0.29.1-4) ... Removing python3-click (8.2.0+0.really.8.1.8-1) ... Removing python3-dateutil (2.9.0-4) ... Removing python3-depinfo (2.2.0-4) ... Removing python3-diskcache (5.6.3-1) ... Removing python3-h11 (0.14.0-1.1) ... Removing python3-idna (3.11-1) ... Removing python3-mdurl (0.1.2-1) ... Removing python3-mpmath (1.4.0-1) ... Removing python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... Removing python3-platformdirs (4.9.2-1) ... Removing python3-pygments (2.19.2+dfsg-1) ... Removing python3-pytz (2025.2-5) ... Removing python3-tabulate (0.9.0-1) ... Removing python3-typing-inspection (0.4.2-1) ... Removing python3-typing-extensions (4.15.0-2) ... Removing python3 (3.13.9-3) ... Removing python3.13 (3.13.12-1) ... Removing python3-minimal (3.13.9-3) ... Removing python3.13-minimal (3.13.12-1) ... Removing libexpat1:amd64 (2.7.4-1) ... Removing libpython3-stdlib:amd64 (3.13.9-3) ... Removing libpython3.13-stdlib:amd64 (3.13.12-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.5.2-3+b1) ... Removing libncursesw6:amd64 (6.6+20251231-1) ... Removing libpython3.13-minimal:amd64 (3.13.12-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.3-4) ... 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 (3.46.1-9) ... Removing media-types (14.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.3-4) ... Processing triggers for libc-bin (2.42-13) ... 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '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', 'libsqlite3-0:amd64', 'libsuitesparseconfig7:amd64', 'libxml2-16: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-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-typing-inspection', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-cobra'] 0m42.6s INFO: Running scripts post_remove 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_remove_exceptions'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_remove_exceptions'] 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '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', 'libsqlite3-0:amd64', 'libsuitesparseconfig7:amd64', 'libxml2-16: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-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-typing-inspection', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m42.7s DUMP: (Reading database ... 4914 files and directories currently installed.) Purging configuration files for ca-certificates (20260223) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove libamd3 which is not installed dpkg: warning: ignoring request to remove libblas3 which is not installed dpkg: warning: ignoring request to remove libcolamd3 which is not installed dpkg: warning: ignoring request to remove libexpat1 which is not installed dpkg: warning: ignoring request to remove libffi8 which is not installed dpkg: warning: ignoring request to remove libgfortran5 which is not installed dpkg: warning: ignoring request to remove libglpk40 which is not installed dpkg: warning: ignoring request to remove libgomp1 which is not installed dpkg: warning: ignoring request to remove liblapack3 which is not installed dpkg: warning: ignoring request to remove libltdl7 which is not installed dpkg: warning: ignoring request to remove libncursesw6 which is not installed dpkg: warning: ignoring request to remove libpython3-stdlib which is not installed dpkg: warning: ignoring request to remove libpython3.13 which is not installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.12-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which is not installed Purging configuration files for libreadline8t64:amd64 (8.3-4) ... dpkg: warning: ignoring request to remove libsqlite3-0 which is not installed dpkg: warning: ignoring request to remove libsuitesparseconfig7 which is not installed dpkg: warning: ignoring request to remove libxml2-16 which is not installed Purging configuration files for media-types (14.0.0) ... Purging configuration files for netbase (6.5) ... Purging configuration files for openssl (3.5.5-1) ... dpkg: warning: ignoring request to remove python-cobra-data which is not installed Purging configuration files for python3 (3.13.9-3) ... dpkg: warning: ignoring request to remove python3-annotated-types which is not installed dpkg: warning: ignoring request to remove python3-anyio which is not installed dpkg: warning: ignoring request to remove python3-certifi which is not installed dpkg: warning: ignoring request to remove python3-click which is not installed dpkg: warning: ignoring request to remove python3-dateutil which is not installed dpkg: warning: ignoring request to remove python3-depinfo which is not installed dpkg: warning: ignoring request to remove python3-diskcache which is not installed dpkg: warning: ignoring request to remove python3-dnspython which is not installed dpkg: warning: ignoring request to remove python3-email-validator which is not installed dpkg: warning: ignoring request to remove python3-h11 which is not installed dpkg: warning: ignoring request to remove python3-httpcore which is not installed dpkg: warning: ignoring request to remove python3-httpx which is not installed dpkg: warning: ignoring request to remove python3-idna which is not installed dpkg: warning: ignoring request to remove python3-linkify-it which is not installed dpkg: warning: ignoring request to remove python3-markdown-it which is not installed dpkg: warning: ignoring request to remove python3-mdurl which is not installed dpkg: warning: ignoring request to remove python3-minimal which is not installed dpkg: warning: ignoring request to remove python3-mpmath which is not installed Purging configuration files for python3-numpy (1:2.3.5+ds-3) ... dpkg: warning: ignoring request to remove python3-numpy-dev which is not installed dpkg: warning: ignoring request to remove python3-optlang which is not installed dpkg: warning: ignoring request to remove python3-pandas which is not installed dpkg: warning: ignoring request to remove python3-pandas-lib which is not installed dpkg: warning: ignoring request to remove python3-platformdirs which is not installed dpkg: warning: ignoring request to remove python3-pydantic which is not installed dpkg: warning: ignoring request to remove python3-pydantic-core which is not installed dpkg: warning: ignoring request to remove python3-pygments which is not installed dpkg: warning: ignoring request to remove python3-pytz which is not installed dpkg: warning: ignoring request to remove python3-rich which is not installed dpkg: warning: ignoring request to remove python3-ruamel.yaml which is not installed dpkg: warning: ignoring request to remove python3-ruamel.yaml.clib which is not installed dpkg: warning: ignoring request to remove python3-sbml5 which is not installed dpkg: warning: ignoring request to remove python3-swiglpk which is not installed Purging configuration files for python3-sympy (1.14.0-2) ... dpkg: warning: ignoring request to remove python3-tabulate which is not installed dpkg: warning: ignoring request to remove python3-typing-extensions which is not installed dpkg: warning: ignoring request to remove python3-typing-inspection which is not installed dpkg: warning: ignoring request to remove python3-uc-micro which is not installed dpkg: warning: ignoring request to remove python3.13 which is not installed Purging configuration files for python3.13-minimal (3.13.12-1) ... Purging configuration files for readline-common (8.3-4) ... 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', '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', 'libsqlite3-0:amd64', 'libsuitesparseconfig7:amd64', 'libxml2-16: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-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-typing-inspection', 'python3-uc-micro', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg', '--purge', 'python3-cobra'] 0m42.7s DUMP: dpkg: warning: ignoring request to remove python3-cobra which is not installed 0m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg', '--purge', 'python3-cobra'] 0m42.7s INFO: Running scripts post_purge 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_purge_exceptions'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_purge_exceptions'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg', '--purge', '--pending'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg', '--purge', '--pending'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg', '--remove', '--pending'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg', '--remove', '--pending'] 0m42.8s INFO: Running scripts post_test 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_test_exceptions'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'tmp/scripts/post_test_exceptions'] 0m42.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m43.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m43.3s DEBUG: No broken symlinks as far as we can find. 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-divert', '--list'] 0m43.3s 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 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'dpkg-divert', '--list'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', 'clean'] 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvfg66lca', 'apt-get', 'clean'] 0m43.4s DEBUG: Recording chroot state 0m43.9s INFO: PASS: Installation and purging test. 0m44.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/shm'] 0m44.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/shm'] 0m44.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/console'] 0m44.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/console'] 0m44.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/ptmx'] 0m44.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/ptmx'] 0m44.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/pts'] 0m44.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/dev/pts'] 0m44.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/proc'] 0m44.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvfg66lca/proc'] 0m44.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m44.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvfg66lca'] 0m44.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpvfg66lca 0m44.6s INFO: PASS: All tests. 0m44.6s INFO: piuparts run ends. ret=0 End: 2026-02-28 04:32:21 GMT